8XR6 | pdb_00008xr6

Cryo-EM structure of cryptophyte photosystem II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex.

Zhang, Y.Z.Li, K.Qin, B.Y.Guo, J.P.Zhang, Q.B.Zhao, D.L.Chen, X.L.Gao, J.Liu, L.N.Zhao, L.S.

(2024) Nat Commun 15: 4999-4999

  • DOI: https://doi.org/10.1038/s41467-024-49453-0
  • Primary Citation of Related Structures:  
    8XR6

  • PubMed Abstract: 

    Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.


  • Organizational Affiliation

    Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. zhangyz@sdu.edu.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A [auth a],
B [auth A]
360Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI41 (Chroomonas placoidea)
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UniProt GroupA0A222AI41
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-4C [auth 0],
G [auth 4]
219Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-1D [auth 1],
J [auth 7]
218Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-2E [auth 2],
K [auth 8]
200Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-3F [auth 3],
L [auth 9]
229Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-5H [auth 5],
MA [auth g]
216Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-6I [auth 6],
VA [auth p]
234Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinHA [auth b],
M [auth B]
509Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AIE3 (Chroomonas placoidea)
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UniProt GroupA0A222AIE3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsbC_CP43IA [auth c],
N [auth C]
473Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI36 (Chroomonas placoidea)
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UniProt GroupA0A222AI36
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinJA [auth d],
O [auth D]
351Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI37 (Chroomonas placoidea)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaKA [auth e],
P [auth E]
84Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI74 (Chroomonas placoidea)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaLA [auth f],
Q [auth F]
42Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI51 (Chroomonas placoidea)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HNA [auth h],
R [auth H]
67Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AIE4 (Chroomonas placoidea)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IOA [auth i],
S [auth I]
38Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI80 (Chroomonas placoidea)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JPA [auth j],
T [auth J]
39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI54 (Chroomonas placoidea)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KQA [auth k],
U [auth K]
45Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AIA0 (Chroomonas placoidea)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LRA [auth l],
V [auth L]
38Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI58 (Chroomonas placoidea)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsbMSA [auth m],
W [auth M]
37Chroomonas placoideaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Psb-gama_linkerTA [auth n],
X [auth N]
297Chroomonas placoideaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
PsbOUA [auth o],
Y [auth O]
300Chroomonas placoideaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsbQWA [auth q],
Z [auth Q]
144Chroomonas placoideaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TAA [auth T],
XA [auth t]
32Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AID2 (Chroomonas placoidea)
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UniProt GroupA0A222AID2
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PsbUBA [auth U],
YA [auth u]
121Chroomonas placoideaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II cytochrome c550CA [auth V],
ZA [auth v]
163Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI35 (Chroomonas placoidea)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
PsbWAB [auth w],
DA [auth W]
130Chroomonas placoideaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XBB [auth x],
EA [auth X]
39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI61 (Chroomonas placoidea)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30CB [auth y],
FA [auth Y]
34Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI69 (Chroomonas placoidea)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZDB [auth z],
GA [auth Z]
62Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI96 (Chroomonas placoidea)
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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BL [auth H]
FN [auth c]
GN [auth c]
IN [auth c]
LO [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth 1]
AF [auth 4]
AH [auth 7]
AJ [auth B]
AK [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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KB [auth a],
LN [auth d],
SK [auth D],
WB [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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DL [auth J]
EL [auth L]
NO [auth j]
OM [auth c]
OO [auth l]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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HN [auth c]
LM [auth b]
ML [auth T]
NM [auth b]
OK [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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NB [auth a],
PN [auth d],
WK [auth D],
ZB [auth A]
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
Query on LHG

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AC [auth A]
AE [auth 3]
AG [auth 5]
AI [auth 8]
CI [auth 9]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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AL [auth F],
NL [auth V],
RP [auth v],
TN [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC2 (Subject of Investigation/LOI)
Query on KC2

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CD [auth 1]
CO [auth g]
DD [auth 1]
EH [auth 7]
FH [auth 7]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0
Query on II0

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BI [auth 9]
CG [auth 6]
FD [auth 1]
FO [auth g]
GD [auth 1]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT
Query on IHT

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IO [auth g]
OP [auth p]
SE [auth 3]
TG [auth 6]
UI [auth 9]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
8CT
Query on 8CT

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CL [auth H]
CN [auth c]
DN [auth c]
ED [auth 1]
EN [auth c]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
OEX
Query on OEX

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EB [auth a],
QB [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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GB [auth a],
SB [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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FB [auth a],
RB [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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HB [auth a],
TB [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Data collection, Database references, Structure summary