8KDE

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.

Li, A.You, T.Pang, X.Wang, Y.Tian, L.Li, X.Liu, Z.

(2024) Nat Commun 15: 5211-5211

  • DOI: https://doi.org/10.1038/s41467-024-49532-2
  • Primary Citation of Related Structures:  
    8KDE, 8ZEE

  • PubMed Abstract: 

    Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q B site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b 559 , potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.


  • Organizational Affiliation

    Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinA [auth B]508Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinB [auth D]352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaC [auth E]82Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48268 (Chlamydomonas reinhardtii)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaD [auth F]44Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HE [auth H]88Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IF [auth I]37Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KG [auth K]46Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LH [auth L]38Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MI [auth M]34Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TJ [auth T]31Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12K [auth V]33Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinL [auth X]101Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A8I846 (Chlamydomonas reinhardtii)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZM [auth Z]62Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Thylakoid enriched factor 14 (TEF14)N [auth G]196Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II repair factor 1 (PRF1)O [auth 3]131Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinP [auth C]461Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1Q [auth A]352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II repair factor 2 (PRF2)R [auth 1]117Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AC [auth C],
BC [auth C],
CC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
GC [auth A],
HA [auth B],
HC [auth A],
IC [auth A],
LB [auth C],
MB [auth C],
NB [auth C],
OB [auth C],
PB [auth C],
QA [auth D],
QB [auth C],
RA [auth D],
RB [auth C],
S [auth B],
SB [auth C],
T [auth B],
TB [auth C],
U [auth B],
UB [auth C],
V [auth B],
VB [auth C],
W [auth B],
WB [auth C],
X [auth B],
XB [auth C],
Y [auth B],
YA [auth D],
Z [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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AB [auth D],
ZA [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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DC [auth C]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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EB [auth K]
KB [auth C]
KC [auth A]
LA [auth B]
OA [auth B]
EB [auth K],
KB [auth C],
KC [auth A],
LA [auth B],
OA [auth B],
XA [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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TA [auth D]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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FB [auth K]
GB [auth L]
HB [auth X]
LC [auth A]
MA [auth B]
FB [auth K],
GB [auth L],
HB [auth X],
LC [auth A],
MA [auth B],
NA [auth B],
PA [auth B],
UA [auth D],
VA [auth D],
WA [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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BB [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR (Subject of Investigation/LOI)
Query on BCR

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CB [auth H]
DB [auth K]
IA [auth B]
JA [auth B]
JB [auth Z]
CB [auth H],
DB [auth K],
IA [auth B],
JA [auth B],
JB [auth Z],
JC [auth A],
KA [auth B],
SA [auth D],
YB [auth C],
ZB [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
VTQ (Subject of Investigation/LOI)
Query on VTQ

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IB [auth X]RRR-ALPHA-TOCOPHERYLQUINONE
C29 H50 O3
LTVDFSLWFKLJDQ-IEOSBIPESA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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EC [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

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FC [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31925024
Chinese Academy of SciencesChinaYSBR-015
Chinese Academy of SciencesChinaXDB37020101

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references