9LE8 | pdb_00009le8

Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex

• PDB DOI: https://doi.org/10.2210/pdb9LE8/pdb
• EM Map EMD-63018: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2025-01-07 Released: 2025-10-08 
• Deposition Author(s): Chen, S.J.B., Wu, C., Wu, J.H., Sui, S.F., Zhang, L.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex

Chen, S.J.B., Wu, C., Wu, J.H., Sui, S.F., Zhang, L.X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 50-mer - A10B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 50-mer - A18B10C4D2E2F2G2H2I2J2K2L2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,323.34 kDa 
• Atom Count: 83,915 
• Modeled Residue Count: 7,854 
• Deposited Residue Count: 8,788 
• Unique protein chains: 22

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	A [auth 9], C [auth AA], E [auth AC], G [auth AE]	266	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for A0A654EYS2 (Arabidopsis thaliana) Explore A0A654EYS2  Go to UniProtKB:  A0A654EYS2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 3, chloroplastic	B [auth 0], F [auth AD]	243	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9S7M0 (Arabidopsis thaliana) Explore Q9S7M0  Go to UniProtKB:  Q9S7M0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	D [auth AB], H [auth AF]	212	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for A0A178WK60 (Arabidopsis thaliana) Explore A0A178WK60  Go to UniProtKB:  A0A178WK60

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	DA [auth AJ], I [auth J]	352	Arabidopsis thaliana	Mutation(s): 0  EC: 1.10.3.9
UniProt
Find proteins for P83755 (Arabidopsis thaliana) Explore P83755  Go to UniProtKB:  P83755

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	EA [auth AK], J [auth O]	508	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56777 (Arabidopsis thaliana) Explore P56777  Go to UniProtKB:  P56777

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	FA [auth AL], K [auth P]	459	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56778 (Arabidopsis thaliana) Explore P56778  Go to UniProtKB:  P56778

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	GA [auth AM], L [auth Q]	352	Arabidopsis thaliana	Mutation(s): 0  EC: 1.10.3.9
UniProt
Find proteins for P56761 (Arabidopsis thaliana) Explore P56761  Go to UniProtKB:  P56761

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	HA [auth e], M [auth E]	83	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56779 (Arabidopsis thaliana) Explore P56779  Go to UniProtKB:  P56779

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	IA [auth f], N [auth F]	39	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62095 (Arabidopsis thaliana) Explore P62095  Go to UniProtKB:  P62095

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 1, chloroplastic	BA [auth AH], JA [auth AN], O [auth V], PA [auth AQ], U [auth p], WA [auth AU]	232	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P04778 (Arabidopsis thaliana) Explore P04778  Go to UniProtKB:  P04778

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	KA [auth AO], P [auth j]	72	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56780 (Arabidopsis thaliana) Explore P56780  Go to UniProtKB:  P56780

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	LA [auth i], Q [auth I]	36	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62100 (Arabidopsis thaliana) Explore P62100  Go to UniProtKB:  P62100

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	MA [auth k], R [auth K]	37	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56782 (Arabidopsis thaliana) Explore P56782  Go to UniProtKB:  P56782

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	NA [auth AP], S [auth o]	38	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P60129 (Arabidopsis thaliana) Explore P60129  Go to UniProtKB:  P60129

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	OA [auth m], T [auth M]	34	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62109 (Arabidopsis thaliana) Explore P62109  Go to UniProtKB:  P62109

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein CP29.1, chloroplastic	QA [auth AR], V [auth q]	250	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q07473 (Arabidopsis thaliana) Explore Q07473  Go to UniProtKB:  Q07473

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein CP26, chloroplastic	RA [auth AS], W [auth v]	232	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9XF89 (Arabidopsis thaliana) Explore Q9XF89  Go to UniProtKB:  Q9XF89

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	SA [auth AT], X [auth AG]	33	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P61839 (Arabidopsis thaliana) Explore P61839  Go to UniProtKB:  P61839

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 5 kDa protein, chloroplastic	TA [auth u], Y [auth U]	28	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39195 (Arabidopsis thaliana) Explore Q39195  Go to UniProtKB:  Q39195

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center W protein, chloroplastic	UA [auth w], Z [auth W]	54	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39194 (Arabidopsis thaliana) Explore Q39194  Go to UniProtKB:  Q39194

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
(thale cress) hypothetical protein	AA [auth X], VA [auth x]	42	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for A0A7G2E9B1 (Arabidopsis thaliana) Explore A0A7G2E9B1  Go to UniProtKB:  A0A7G2E9B1

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	CA [auth AI], XA [auth AV]	62	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56790 (Arabidopsis thaliana) Explore P56790  Go to UniProtKB:  P56790

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	BJ [auth j], DP [auth AO], HG [auth J], JG [auth J], JM [auth AJ], YH [auth P], YL [auth AJ], YN [auth AL], ZN [auth AL]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL	BE [auth AD], BK [auth q], BP [auth AN], CB [auth 9], CD [auth AB], CE [auth AD], CK [auth q], DB [auth 9], DD [auth AB], DK [auth q], DQ [auth AR], EB [auth 9], ED [auth AB], EQ [auth AR], FB [auth 9], FD [auth AB], FJ [auth p], FQ [auth AR], GB [auth 9], GC [auth 0], GE [auth AD], HC [auth AA], HE [auth AD], HF [auth AE], HL [auth AH], HP [auth AQ], IE [auth AD], IF [auth AE], IR [auth AU], JF [auth AF], JJ [auth p], JK [auth q], KI [auth V], KJ [auth p], LC [auth AA], LD [auth AC], LJ [auth p], LL [auth AH], LO [auth AN], LP [auth AQ], LQ [auth AR], MC [auth AA], MJ [auth p], ML [auth AH], MP [auth AQ], MR [auth AU], NC [auth AA], NF [auth AF], NJ [auth p], NL [auth AH], NP [auth AQ], NR [auth AU], OC [auth AA], OF [auth AF], OI [auth V], OL [auth AH], OP [auth AQ], OR [auth AU], PD [auth AC], PF [auth AF], PI [auth V], PO [auth AN], PP [auth AQ], PR [auth AU], QB [auth 0], QD [auth AC], QF [auth AF], QI [auth V], QK [auth v], QO [auth AN], RD [auth AC], RE [auth AD], RI [auth V], RO [auth AN], RQ [auth AS], SD [auth AC], SE [auth AE], SO [auth AN], UB [auth 0], UK [auth v], VB [auth 0], VK [auth v], VQ [auth AS], WB [auth 0], WE [auth AE], WK [auth v], WQ [auth AS], XB [auth 0], XC [auth AA], XE [auth AE], XQ [auth AS], YA [auth 9], YC [auth AB], YE [auth AE], ZI [auth V]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	AB [auth 9], AC [auth 0], AD [auth AB], AF [auth AE], AG [auth J], AK [auth q], AL [auth v], AN [auth AK], AQ [auth AR], AR [auth AS], BB [auth 9], BC [auth 0], BD [auth AB], BF [auth AE], BI [auth Q], BL [auth v], BM [auth AJ], BN [auth AK], BQ [auth AR], BR [auth AS], CC [auth 0], CF [auth AE], CJ [auth K], CL [auth v], CM [auth AJ], CQ [auth AR], CR [auth AS], DE [auth AD], DF [auth AE], DG [auth J], DI [auth Q], DM [auth AJ], DR [auth AS], EE [auth AD], EI [auth Q], EK [auth q], EO [auth AM], FE [auth AD], FK [auth q], FO [auth AM], GD [auth AB], GJ [auth p], GK [auth q], GM [auth AJ], GQ [auth AR], HB [auth 9], HD [auth AB], HJ [auth p], HK [auth q], HQ [auth AR], IB [auth 9], IC [auth AA], ID [auth AB], IJ [auth p], IK [auth q], IL [auth AH], IP [auth AQ], IQ [auth AR], JB [auth 9], JC [auth AA], JE [auth AD], JH [auth P], JL [auth AH], JN [auth AL], JP [auth AQ], JQ [auth AR], JR [auth AU], KB [auth 9], KC [auth AA], KE [auth AD], KF [auth AF], KG [auth O], KH [auth P], KL [auth AH], KN [auth AL], KP [auth AQ], KQ [auth AR], KR [auth AU], LB [auth 9], LE [auth AD], LF [auth AF], LG [auth O], LH [auth P], LI [auth V], LN [auth AL], LR [auth AU], MD [auth AC], ME [auth AD], MF [auth AF], MG [auth O], MH [auth P], MI [auth V], MM [auth AK], MN [auth AL], MO [auth AN], ND [auth AC], NE [auth AD], NG [auth O], NH [auth P], NI [auth V], NM [auth AK], NN [auth AL], NO [auth AN], OD [auth AC], OG [auth O], OH [auth P], OJ [auth p], OK [auth q], OM [auth AK], ON [auth AL], OO [auth AN], PC [auth AA], PG [auth O], PH [auth P], PJ [auth p], PL [auth AH], PM [auth AK], PN [auth AL], PQ [auth AR], QC [auth AA], QG [auth O], QH [auth P], QJ [auth p], QL [auth AH], QM [auth AK], QN [auth AL], QP [auth AQ], QR [auth AU], RB [auth 0], RC [auth AA], RF [auth AF], RG [auth O], RH [auth P], RJ [auth p], RK [auth v], RL [auth AH], RM [auth AK], RN [auth AL], RP [auth AQ], RR [auth AU], SB [auth 0], SC [auth AA], SF [auth AF], SG [auth O], SH [auth P], SI [auth V], SK [auth v], SL [auth AH], SM [auth AK], SN [auth AL], SP [auth AQ], SQ [auth AS], SR [auth AU], TB [auth 0], TC [auth AA], TD [auth AC], TE [auth AE], TG [auth O], TH [auth P], TI [auth V], TK [auth v], TL [auth AH], TM [auth AK], TN [auth AL], TO [auth AN], TP [auth AQ], TQ [auth AS], TR [auth AU], UD [auth AC], UE [auth AE], UG [auth O], UH [auth P], UI [auth V], UM [auth AK], UN [auth AL], UO [auth AN], UP [auth AQ], UQ [auth AS], UR [auth AU], VD [auth AC], VE [auth AE], VG [auth O], VI [auth V], VM [auth AK], VN [auth AL], VO [auth AN], WD [auth AC], WF [auth AF], WG [auth O], WJ [auth p], WM [auth AK], WO [auth AN], XD [auth AC], XG [auth O], XJ [auth q], XK [auth v], XM [auth AK], XO [auth AN], YB [auth 0], YG [auth O], YJ [auth q], YK [auth v], YM [auth AK], YQ [auth AS], ZA [auth 9], ZB [auth 0], ZC [auth AB], ZE [auth AE], ZF [auth J], ZG [auth O], ZJ [auth q], ZK [auth v], ZM [auth AK], ZP [auth AR], ZQ [auth AS]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	BG [auth J], CG [auth J], EM [auth AJ], FM [auth AJ]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	CI [auth Q], CO [auth AM], DJ [auth o], EJ [auth M], FP [auth AP], GG [auth J], GP [auth m], IM [auth AJ]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AI [auth P], BO [auth AL], DH [auth O], FG [auth J], FN [auth AK], HH [auth O], HI [auth Q], IN [auth AL], IO [auth AM], KM [auth AK]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	FI [auth Q], GO [auth AM]	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	AO [auth AL], AP [auth AN], EH [auth O], FC [auth 0], FH [auth O], GH [auth O], GI [auth Q], GL [auth W], GN [auth AK], HN [auth AK], HO [auth AM], HR [auth w], MK [auth q], PK [auth v], QE [auth AD], QQ [auth AS], VJ [auth p], WL [auth AH], YI [auth V], YP [auth AQ], YR [auth AU], ZH [auth P]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	JI [auth F], KO [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XAT	KD [auth AB], NK [auth q], OQ [auth AR], PB [auth 9], VF [auth AF]	(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	AE [auth AC], FL [auth v], GF [auth AE], GR [auth AS], LK [auth q], NQ [auth AR], OB [auth 9], UJ [auth p], WC [auth AA], XP [auth AQ], XR [auth AU]	(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	DC [auth 0], DL [auth v], EC [auth 0], EF [auth AE], EL [auth v], ER [auth AS], FF [auth AE], FR [auth AS], KK [auth q], MB [auth 9], MQ [auth AR], NB [auth 9], OE [auth AD], PE [auth AD], SJ [auth p], TF [auth AF], TJ [auth p], UC [auth AA], UL [auth AH], VC [auth AA], VL [auth AH], VP [auth AQ], VR [auth AU], WI [auth V], WP [auth AQ], WR [auth AU], XI [auth V], YD [auth AC], YO [auth AN], ZD [auth AC], ZO [auth AN]	(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)	AH [auth O], AJ [auth j], BH [auth O], CH [auth O], CN [auth AK], CP [auth AO], DN [auth AK], EG [auth J], EN [auth AK], EP [auth k], HM [auth AJ], IH [auth O], II [auth F], JD [auth AB], JO [auth f], LM [auth AK], UF [auth AF], VH [auth P], WH [auth P], WN [auth AL], XH [auth P], XL [auth AI], XN [auth AL], ZR [auth AV]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
OEX	XF [auth J], ZL [auth AJ]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	DO [auth AM], IG [auth J]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	AM [auth AJ], YF [auth J]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Chen, S.J.B., Wu, C., Wu, J.H., Sui, S.F., Zhang, L.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release