8ZEE | pdb_00008zee

Cryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth M]	SCOP2B Superfamily	Photosystem II reaction center protein M, PsbM	8094094	3001573	SCOP2B (2022-06-29)
H [auth L]	SCOP2B Superfamily	Photosystem II reaction center protein L, PsbL	8094509	3001523	SCOP2B (2022-06-29)
G [auth K]	SCOP2B Superfamily	Photosystem II reaction center protein K, PsbK	8093946	3001585	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	Photosystem II reaction center protein I, PsbI	8094000	3001590	SCOP2B (2022-06-29)
E [auth H]	SCOP2B Superfamily	Photosystem II 10 kDa phosphoprotein PsbH	8094651	3001547	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Cytochrome b559 subunits	8093904	3001602	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Cytochrome b559 subunits	8094631	3001602	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8094383	3000736	SCOP2B (2022-06-29)
O [auth A]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8094419	3000736	SCOP2B (2022-06-29)
N [auth C]	SCOP2B Superfamily	Photosystem II antenna protein-like	8094477	3001674	SCOP2B (2022-06-29)
M [auth Z]	SCOP2B Superfamily	PsbZ-like	8094160	3001624	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Photosystem II antenna protein-like	8094573	3001674	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth L]	PF02419	PsbL protein (PsbL)	PsbL protein	-	Family
F [auth I]	PF02532	Photosystem II reaction centre I protein (PSII 4.8 kDa protein) (PsbI)	Photosystem II reaction centre I protein (PSII 4.8 kDa protein)	-	Family
E [auth H]	PF00737	Photosystem II 10 kDa phosphoprotein (PsbH)	Photosystem II 10 kDa phosphoprotein	-	Family
C [auth E]	PF00283	Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits (Cytochrom_B559)	Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits	-	Family
C [auth E]	PF00284	Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit (Cytochrom_B559a)	Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit	-	Family
B [auth D]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
O [auth A]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
N [auth C]	PF00421	Photosystem II protein (PSII)	Photosystem II protein	-	Family
M [auth Z]	PF01737	YCF9 (Ycf9)	YCF9	-	Family
L [auth X]	PF06596	Photosystem II reaction centre X protein (PsbX) (PsbX)	Photosystem II reaction centre X protein (PsbX)	-	Family
J [auth T]	PF01405	Photosystem II reaction centre T protein (PsbT)	Photosystem II reaction centre T protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth M]	Photosystem II reaction center protein M	-	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
H [auth L]	Photosystem II reaction center protein L	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
G [auth K]	Photosystem II reaction center protein K	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
F [auth I]	Photosystem II reaction center protein I	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
E [auth H]	Photosystem II reaction center protein H	ion binding binding anion binding phosphate ion binding small molecule binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
D [auth F]	Cytochrome b559 subunit beta	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
C [auth E]	Cytochrome b559 subunit alpha	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
B [auth D]	Photosystem II D2 protein	oxidoreductase activity oxygen evolving activity catalytic activity chlorophyll binding binding tetrapyrrole binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
P [auth 1]	Chains: 1	-	-	-
O [auth A]	Photosystem II protein D1	oxidoreductase activity oxygen evolving activity catalytic activity chlorophyll binding binding tetrapyrrole binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity, acting on diphenols and related substances as donors	response to stimulus response to chemical response to stress response to herbicide response to toxic substance photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
N [auth C]	Photosystem II CP43 reaction center protein	chlorophyll binding binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
M [auth Z]	Photosystem II reaction center protein Z	-	photosynthesis metabolic process cellular process regulation of biological process regulation of cellular process regulation of photosynthesis photosynthesis, light reaction photosystem II stabilization regulation of photosynthesis, light reaction biological regulation regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of metabolic process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
L [auth X]	4.1 kDa photosystem II subunit	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid
K [auth V]	Photosystem II reaction center protein Psb30	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
J [auth T]	Photosystem II reaction center protein T	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
A [auth B]	Photosystem II CP47 reaction center protein	chlorophyll binding binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth M]	IPR007826	Photosystem II PsbM	Family
I [auth M]	IPR037269	Photosystem II PsbM superfamily	Homologous Superfamily
H [auth L]	IPR003372	Photosystem II PsbL	Family
H [auth L]	IPR037266	Photosystem II PsbL superfamily	Homologous Superfamily
G [auth K]	IPR037270	Photosystem II PsbK superfamily	Homologous Superfamily
G [auth K]	IPR003687	Photosystem II PsbK	Family
F [auth I]	IPR037271	Photosystem II PsbI superfamily	Homologous Superfamily
F [auth I]	IPR003686	Photosystem II PsbI	Family
E [auth H]	IPR036863	Photosystem II reaction centre protein H superfamily	Homologous Superfamily
E [auth H]	IPR001056	Photosystem II reaction centre protein H	Family
D [auth F]	IPR006241	Photosystem II cytochrome b559, beta subunit	Family
D [auth F]	IPR013081	Photosystem II cytochrome b559, N-terminal	Domain
D [auth F]	IPR006216	Photosystem II cytochrome b559, conserved site	Conserved Site
C [auth E]	IPR013081	Photosystem II cytochrome b559, N-terminal	Domain
C [auth E]	IPR006217	Photosystem II cytochrome b559, alpha subunit	Family
C [auth E]	IPR013082	Photosystem II cytochrome b559, alpha subunit, lumenal region	Domain
C [auth E]	IPR037025	Photosystem II cytochrome b559, alpha subunit superfamily	Homologous Superfamily
C [auth E]	IPR006216	Photosystem II cytochrome b559, conserved site	Conserved Site
B [auth D]	IPR005868	Photosystem II D2	Family
B [auth D]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
B [auth D]	IPR000484	Photosynthetic reaction centre, L/M	Family
B [auth D]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
B [auth D]	IPR055266	Photosystem II protein D1/D2	Family
O [auth A]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
O [auth A]	IPR005867	Photosystem II protein D1	Family
O [auth A]	IPR000484	Photosynthetic reaction centre, L/M	Family
O [auth A]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
O [auth A]	IPR055266	Photosystem II protein D1/D2	Family
N [auth C]	IPR036001	Photosystem antenna protein-like superfamily	Homologous Superfamily
N [auth C]	IPR000932	Photosystem antenna protein-like	Family
N [auth C]	IPR005869	Photosystem II CP43 reaction centre protein	Family
N [auth C]	IPR044900	Photosystem II CP43 reaction centre protein superfamily	Homologous Superfamily
M [auth Z]	IPR036512	Photosystem II PsbZ superfamily	Homologous Superfamily
M [auth Z]	IPR002644	Photosystem II PsbZ, reaction centre	Family
L [auth X]	IPR009518	Photosystem II PsbX	Family
K [auth V]	IPR010284	Photosystem II reaction center protein Ycf12	Family
J [auth T]	IPR001743	Photosystem II PsbT	Family
J [auth T]	IPR037268	Photosystem II PsbT superfamily	Homologous Superfamily
A [auth B]	IPR036001	Photosystem antenna protein-like superfamily	Homologous Superfamily
A [auth B]	IPR000932	Photosystem antenna protein-like	Family
A [auth B]	IPR017486	Photosystem II CP47 reaction centre protein	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth D], C [auth E], D [auth F], E [auth H] A [auth B], B [auth D], C [auth E], D [auth F], E [auth H], F [auth I], G [auth K], H [auth L], I [auth M], J [auth T], K [auth V], L [auth X], M [auth Z], N [auth C], O [auth A]	PDBTM	Annotated as membrane protein by PDBTM