9IOX | pdb_00009iox

Cryo-EM structure of a TEF30-associated intermediate PSII core dimer complex, type II, from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Roles of multiple TEF30-associated intermediate complexes in the repair and reassembly of photosystem II in Chlamydomonas reinhardtii.

Wang, Y.Wang, C.Li, A.Liu, Z.

(2025) Nat Plants 11: 1455-1469

  • DOI: https://doi.org/10.1038/s41477-025-02036-3
  • Primary Citation of Related Structures:  
    9IIU, 9IMN, 9IOX, 9IS4

  • PubMed Abstract: 

    During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a sophisticated biological process assisted by numerous auxiliary proteins. Here we report the cryogenic electron microscopy structures of four PSII-repair complexes from Chlamydomonas reinhardtii associated with the Thylakoid Enriched Fraction 30 (TEF30, an orthologue of plant MET1) protein-namely, a TEF30-PSII core monomer (TEF30-C), two types of TEF30-PSII core dimers (types I and II, TEF30 2 -C 2 -I and TEF30 2 -C 2 -II) and a TEF30-C 2 S-type PSII-LHCII supercomplex (TEF30-C 2 S; S, strongly associated light-harvesting complex II trimer). TEF30 mediates the assembly of CP43 with the RC47 module by clamping on the stromal surfaces and prevents the premature association of peripheral antennae with PSII-C. In the transition from TEF30 2 -C 2 -I to TEF30 2 -C 2 -II, TEF30-C 2 S and mature C 2 S 2 , one PSII core slides along the dimerization interface against the adjacent one by 22-35 Å, generating a zigzagged surface for accommodating the peripheral antennae. These results suggest that the PSII repair process undergoes multiple TEF30-mediated intermediate states to form intact PSII-LHCII supercomplexes.


  • 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, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Q [auth a]
327Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
R [auth b]
480Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for P37255 (Chlamydomonas reinhardtii)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
S [auth c]
450Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
T [auth d]
351Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
U [auth e]
74Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
V [auth f]
31Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PDZ domain-containing proteinG,
W [auth g]
195Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_01g031100v5
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HH,
X [auth h]
71Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein II,
Y [auth i]
34Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K],
Z [auth k]
37Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LAA [auth l],
K [auth L]
38Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MBA [auth m],
L [auth M]
27Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TCA [auth t],
M [auth T]
28Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30DA [auth v],
N [auth V]
31Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chloroplast photosystem II subunit XEA [auth x],
O [auth X]
32Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZFA [auth z],
P [auth Z]
61Chlamydomonas reinhardtiiMutation(s): 0 
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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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DC [auth C]
EC [auth C]
FC [auth C]
RE [auth c]
SE [auth c]
DC [auth C],
EC [auth C],
FC [auth C],
RE [auth c],
SE [auth c],
TE [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AB [auth B]
AF [auth d]
BB [auth B]
BD [auth a]
CB [auth B]
AB [auth B],
AF [auth d],
BB [auth B],
BD [auth a],
CB [auth B],
CE [auth c],
DB [auth B],
DE [auth c],
EB [auth B],
EE [auth c],
FB [auth B],
FD [auth b],
FE [auth c],
GD [auth b],
GE [auth c],
HA [auth A],
HD [auth b],
HE [auth c],
IA [auth A],
IC [auth D],
ID [auth b],
IE [auth c],
JD [auth b],
JE [auth c],
KA [auth A],
KD [auth b],
KE [auth c],
LC [auth D],
LD [auth b],
LE [auth c],
MC [auth D],
MD [auth b],
ME [auth c],
NB [auth C],
ND [auth b],
NE [auth c],
OB [auth C],
OD [auth b],
OE [auth c],
PB [auth C],
PD [auth b],
QA [auth B],
QB [auth C],
QD [auth b],
RA [auth B],
RB [auth C],
RD [auth b],
SA [auth B],
SB [auth C],
SD [auth b],
TA [auth B],
TB [auth C],
TD [auth b],
UA [auth B],
UB [auth C],
UD [auth b],
VA [auth B],
VB [auth C],
WA [auth B],
WB [auth C],
WE [auth d],
XA [auth B],
XB [auth C],
YA [auth B],
YB [auth C],
YC [auth a],
ZA [auth B],
ZB [auth C],
ZC [auth a],
ZE [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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AD [auth a],
JA [auth A],
JC [auth D],
XE [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AE [auth c],
MB [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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BE [auth c]
EF [auth d]
GC [auth C]
GF [auth h]
JB [auth B]
BE [auth c],
EF [auth d],
GC [auth C],
GF [auth h],
JB [auth B],
MA [auth A],
QC [auth D],
RC [auth D],
UE [auth c],
XD [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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CF [auth d],
OC [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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DD [auth a]
DF [auth d]
ED [auth a]
IF [auth l]
JF [auth x]
DD [auth a],
DF [auth d],
ED [auth a],
IF [auth l],
JF [auth x],
KB [auth B],
LB [auth B],
NA [auth A],
OA [auth A],
PC [auth D],
UC [auth L],
VC [auth X],
YD [auth b],
ZD [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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FF [auth e],
SC [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR (Subject of Investigation/LOI)
Query on BCR

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AC [auth C]
BC [auth C]
BF [auth d]
CC [auth C]
CD [auth a]
AC [auth C],
BC [auth C],
BF [auth d],
CC [auth C],
CD [auth a],
GB [auth B],
HB [auth B],
HF [auth k],
IB [auth B],
KF [auth x],
LA [auth A],
LF [auth z],
NC [auth D],
PA [auth A],
PE [auth c],
QE [auth c],
TC [auth K],
VD [auth b],
WC [auth X],
WD [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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HC [auth C],
VE [auth c]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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KC [auth D],
YE [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

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GA [auth A],
XC [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-30
    Changes: Data collection, Database references