9IS4 | pdb_00009is4

Cryo-EM structure of a TEF30-associated intermediate C2S-type PSII-LHCII supercomplex from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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
PDZ domain-containing proteinA [auth 1]159Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_01g031100v5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1B [auth A],
W [auth a]
335Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinC [auth B],
X [auth b]
481Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinD [auth C],
Y [auth c]
449Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinE [auth D],
Z [auth d]
351Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaAA [auth e],
F [auth E]
75Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaBA [auth f],
G [auth F]
31Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticH [auth G]219Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HCA [auth h],
I [auth H]
69Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IDA [auth i],
J [auth I]
35Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KEA [auth k],
K
37Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LFA [auth l],
L
37Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MGA [auth m],
M
31Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic219Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1, chloroplastic240Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth S]250Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TIA [auth t],
Q [auth T]
30Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30JA [auth v],
R [auth V]
32Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticS [auth W]56Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chloroplast photosystem II subunit XKA [auth x],
T [auth X]
32Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticU [auth Y]220Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
V [auth Z]
61Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29HA [auth r]201Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 16 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]
GF [auth W]
HF [auth Y]
DC [auth C],
EC [auth C],
FC [auth C],
GF [auth W],
HF [auth Y],
UH [auth c],
VH [auth c],
WH [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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AD [auth G]
AE [auth N]
BD [auth G]
BE [auth N]
CD [auth G]
AD [auth G],
AE [auth N],
BD [auth G],
BE [auth N],
CD [auth G],
DD [auth G],
JF [auth Y],
LE [auth S],
ND [auth G],
NF [auth Y],
OF [auth Y],
PF [auth Y],
QE [auth S],
QF [auth Y],
QI [auth r],
RE [auth S],
RI [auth r],
SE [auth S],
SI [auth r],
TD [auth N],
VC [auth G],
XD [auth N],
YD [auth N],
ZC [auth G],
ZD [auth N]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AB [auth B]
AH [auth b]
BB [auth B]
BG [auth a]
BI [auth d]
AB [auth B],
AH [auth b],
BB [auth B],
BG [auth a],
BI [auth d],
CB [auth B],
CE [auth N],
CG [auth a],
CI [auth d],
DB [auth B],
DE [auth N],
EB [auth B],
ED [auth G],
EE [auth N],
EG [auth a],
FB [auth B],
FD [auth G],
FE [auth N],
GB [auth B],
GD [auth G],
GE [auth N],
GH [auth c],
HB [auth B],
HD [auth G],
HH [auth c],
IB [auth B],
ID [auth G],
IH [auth c],
JH [auth c],
KC [auth D],
KF [auth Y],
KH [auth c],
LF [auth Y],
LG [auth b],
LH [auth c],
ME [auth S],
MF [auth Y],
MG [auth b],
MH [auth c],
NA [auth A],
NB [auth C],
NC [auth D],
NE [auth S],
NG [auth b],
NH [auth c],
NI [auth r],
OA [auth A],
OB [auth C],
OC [auth D],
OE [auth S],
OG [auth b],
OH [auth c],
OI [auth r],
PB [auth C],
PE [auth S],
PG [auth b],
PH [auth c],
PI [auth r],
QA [auth A],
QB [auth C],
QG [auth b],
QH [auth c],
RB [auth C],
RF [auth Y],
RG [auth b],
RH [auth c],
SB [auth C],
SF [auth Y],
SG [auth b],
SH [auth c],
TA [auth B],
TB [auth C],
TE [auth S],
TF [auth Y],
TG [auth b],
TI [auth r],
UA [auth B],
UB [auth C],
UD [auth N],
UE [auth S],
UF [auth Y],
UG [auth b],
UI [auth r],
VA [auth B],
VB [auth C],
VD [auth N],
VE [auth S],
VF [auth Y],
VG [auth b],
WA [auth B],
WB [auth C],
WC [auth G],
WD [auth N],
WE [auth S],
WG [auth b],
XA [auth B],
XB [auth C],
XC [auth G],
XE [auth S],
XG [auth b],
YA [auth B],
YB [auth C],
YC [auth G],
YE [auth S],
YG [auth b],
ZA [auth B],
ZB [auth C],
ZG [auth b],
ZH [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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AI [auth d],
DG [auth a],
LC [auth D],
PA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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GG [auth a],
SA [auth A],
YI [auth t]
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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EH [auth b]
FF [auth W]
GC [auth C]
HG [auth a]
HI [auth d]
EH [auth b],
FF [auth W],
GC [auth C],
HG [auth a],
HI [auth d],
II [auth d],
LB [auth B],
QD [auth H],
TC [auth D],
XH [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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EI [auth d],
QC [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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CF [auth S]
FH [auth b]
FI [auth d]
GI [auth d]
HC [auth C]
CF [auth S],
FH [auth b],
FI [auth d],
GI [auth d],
HC [auth C],
JG [auth a],
KE [auth N],
KG [auth a],
MB [auth B],
MD [auth G],
MI [auth l],
RC [auth D],
RD [auth L],
SC [auth D],
ZF [auth Y]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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JI [auth f],
UC [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XAT (Subject of Investigation/LOI)
Query on XAT

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IF [auth Y],
OD [auth G],
SD [auth N],
VI [auth r]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
NEX (Subject of Investigation/LOI)
Query on NEX

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BF [auth S],
JE [auth N],
LD [auth G],
WI [auth r],
YF [auth Y]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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AF [auth S]
HE [auth N]
IE [auth N]
JD [auth G]
KD [auth G]
AF [auth S],
HE [auth N],
IE [auth N],
JD [auth G],
KD [auth G],
WF [auth Y],
XF [auth Y],
ZE [auth S]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AC [auth C]
AJ [auth z]
BC [auth C]
BH [auth b]
CC [auth C]
AC [auth C],
AJ [auth z],
BC [auth C],
BH [auth b],
CC [auth C],
CH [auth b],
DH [auth b],
DI [auth d],
EF [auth V],
FG [auth a],
JB [auth B],
KB [auth B],
KI [auth h],
LI [auth k],
PC [auth D],
PD [auth H],
RA [auth A],
TH [auth c],
XI [auth t],
ZI [auth v]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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DF [auth S],
IC [auth C],
JC [auth C],
YH [auth c]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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