9I4T | pdb_00009i4t

Photosystem II from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb9I4T/pdb
• EM Map EMD-52620: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Arabidopsis thaliana
• Mutation(s): Yes 


• Deposited: 2025-01-26 Released: 2026-03-25 
• Deposition Author(s): Forsman, J.A., Graca, A.T., Hussein, R., Hall, M., Messinger, J., Schroder, W.P., Aydin, A.O.
• Funding Organization(s): Sven och Lilly Lawskis fond for naturvetenskaplig forskning, Swedish Research Council, Carl Trygger Foundation, Kempe Foundation, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Photosystem II from Arabidopsis thaliana

Forsman, J.A., Graca, A.T., Hussein, R., Hall, M., Messinger, J., Schroder, W.P., Aydin, A.O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 50-mer - A6B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 50-mer - A12B8C4D2E2F2G2H2I2J2K2L2M2N2O2P2 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 1,288.9 kDa 
• Atom Count: 76,824 
• Modeled Residue Count: 7,548 
• Deposited Residue Count: 9,452 
• Unique protein chains: 24

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A, Z [auth a]	353	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	AA [auth b], B	508	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56777 (Arabidopsis thaliana) Explore P56777  Go to UniProtKB:  P56777

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	BA [auth c], C	473	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56778 (Arabidopsis thaliana) Explore P56778  Go to UniProtKB:  P56778

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	CA [auth d], D	353	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	DA [auth e], E	83	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56779 (Arabidopsis thaliana) Explore P56779  Go to UniProtKB:  P56779

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	EA [auth f], F	39	Arabidopsis thaliana	Mutation(s): 1
UniProt
Find proteins for P62095 (Arabidopsis thaliana) Explore P62095  Go to UniProtKB:  P62095

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 1, chloroplastic	FA [auth g], G, MA [auth n], N	267	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P04778 (Arabidopsis thaliana) Explore P04778  Go to UniProtKB:  P04778

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	GA [auth h], H	73	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56780 (Arabidopsis thaliana) Explore P56780  Go to UniProtKB:  P56780

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	HA [auth i], I	36	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62100 (Arabidopsis thaliana) Explore P62100  Go to UniProtKB:  P62100

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	IA [auth j], J	40	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56781 (Arabidopsis thaliana) Explore P56781  Go to UniProtKB:  P56781

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	JA [auth k], K	61	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56782 (Arabidopsis thaliana) Explore P56782  Go to UniProtKB:  P56782

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	KA [auth l], L	38	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P60129 (Arabidopsis thaliana) Explore P60129  Go to UniProtKB:  P60129

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	LA [auth m], M	34	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62109 (Arabidopsis thaliana) Explore P62109  Go to UniProtKB:  P62109

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-evolving enhancer protein 1-1, chloroplastic	NA [auth o], O	332	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P23321 (Arabidopsis thaliana) Explore P23321  Go to UniProtKB:  P23321

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-evolving enhancer protein 2-1, chloroplastic	OA [auth p], P	263	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q42029 (Arabidopsis thaliana) Explore Q42029  Go to UniProtKB:  Q42029

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-evolving enhancer protein 3-1, chloroplastic	PA [auth q], Q	224	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9XFT3 (Arabidopsis thaliana) Explore Q9XFT3  Go to UniProtKB:  Q9XFT3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein CP29.1, chloroplastic	QA [auth r], R	290	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q07473 (Arabidopsis thaliana) Explore Q07473  Go to UniProtKB:  Q07473

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein CP26, chloroplastic	RA [auth s], S	280	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9XF89 (Arabidopsis thaliana) Explore Q9XF89  Go to UniProtKB:  Q9XF89

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	SA [auth t], T	33	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P61839 (Arabidopsis thaliana) Explore P61839  Go to UniProtKB:  P61839

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 5 kDa protein, chloroplastic	TA [auth u], U	103	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39195 (Arabidopsis thaliana) Explore Q39195  Go to UniProtKB:  Q39195

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center W protein, chloroplastic	UA [auth w], V [auth W]	133	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39194 (Arabidopsis thaliana) Explore Q39194  Go to UniProtKB:  Q39194

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Expressed protein	VA [auth x], W [auth X]	116	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SKI3 (Arabidopsis thaliana) Explore Q9SKI3  Go to UniProtKB:  Q9SKI3

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 2.1, chloroplastic	WA [auth y], X [auth Y]	265	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SHR7 (Arabidopsis thaliana) Explore Q9SHR7  Go to UniProtKB:  Q9SHR7

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	XA [auth z], Y [auth Z]	62	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P56790 (Arabidopsis thaliana) Explore P56790  Go to UniProtKB:  P56790

Small Molecules

Ligands 18 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD (Subject of Investigation/LOI)	CC [auth B], HJ [auth c], HN [auth y], JJ [auth c], NC [auth C], OC [auth C], OI [auth b], RC [auth C], RI [auth c], SG [auth Y]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL	AF [auth N], AL [auth n], BF [auth N], BL [auth n], BN [auth y], CL [auth n], CN [auth y], DH [auth Y], DK [auth g], DM [auth r], EE [auth G], EF [auth R], EN [auth y], FL [auth n], FM [auth r], GH [auth Y], HG [auth S], HH [auth Y], HK [auth g], IG [auth S], IK [auth g], IM [auth s], JK [auth g], KK [auth g], LG [auth S], LN [auth y], ML [auth n], ND [auth G], NE [auth N], NL [auth n], NN [auth y], OE [auth N], OL [auth r], PD [auth G], PF [auth R], PK [auth g], RD [auth G], RG [auth Y], SF [auth R], SM [auth s], UE [auth N], VD [auth G], VE [auth N], VF [auth R], VM [auth s], WG [auth Y], WL [auth r], WM [auth s], XD [auth G], XF [auth S]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	AB [auth A], AC [auth B], AD [auth D], AE [auth G], AH [auth Y], AI [auth b], AJ [auth c], AK [auth g], AM [auth r], BH [auth Y], BI [auth b], BK [auth g], BM [auth r], CB [auth A], CF [auth N], CG [auth S], CH [auth Y], CI [auth b], CM [auth r], DE [auth G], DF [auth N], DG [auth S], DI [auth b], DJ [auth c], DL [auth n], DN [auth y], EG [auth S], EI [auth b], EJ [auth c], EK [auth g], EL [auth n], EM [auth r], FD [auth D], FE [auth G], FF [auth R], FG [auth S], FH [auth Y], FI [auth b], FJ [auth c], FN [auth y], GG [auth S], GI [auth b], GJ [auth c], GL [auth n], GM [auth s], HI [auth b], IC [auth C], ID [auth D], II [auth b], IJ [auth c], IN [auth y], JB [auth B], JC [auth C], JF [auth R], JG [auth S], JH [auth a], JL [auth n], JM [auth s], JN [auth y], KB [auth B], KC [auth C], KF [auth R], KG [auth S], KI [auth b], KJ [auth c], KM [auth s], LB [auth B], LC [auth C], LD [auth D], LF [auth R], LI [auth b], LK [auth g], LM [auth s], MB [auth B], MC [auth C], MF [auth R], MI [auth b], MM [auth s], MN [auth y], NB [auth B], NF [auth R], NJ [auth d], NK [auth g], OB [auth B], OD [auth G], OJ [auth d], OK [auth g], ON [auth y], PB [auth B], PC [auth C], PM [auth s], PN [auth y], QC [auth C], QD [auth G], QE [auth N], QF [auth R], QG [auth Y], QH [auth a], QL [auth r], QM [auth s], QN [auth y], RB [auth B], RE [auth N], RF [auth R], SB [auth B], SD [auth G], SE [auth N], SH [auth a], SI [auth c], SL [auth r], TB [auth B], TC [auth C], TD [auth G], TE [auth N], TF [auth R], TI [auth c], TL [auth r], TM [auth s], UB [auth B], UC [auth C], UF [auth R], UG [auth Y], UI [auth c], UM [auth s], VB [auth B], VC [auth C], VH [auth b], VI [auth c], VJ [auth d], VL [auth r], WE [auth N], WH [auth b], WI [auth c], WK [auth n], XB [auth B], XC [auth C], XE [auth N], XG [auth Y], XK [auth n], XL [auth r], YB [auth B], YC [auth C], YF [auth S], YH [auth b], YI [auth c], YJ [auth g], YK [auth n], YL [auth r], ZB [auth B], ZC [auth C], ZD [auth G], ZF [auth S], ZG [auth Y], ZH [auth b], ZJ [auth g], ZK [auth n]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	BB [auth A], CD [auth D], RH [auth a], RJ [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)	DC [auth B], EB [auth A], HB [auth A], KH [auth a], PG [auth W], PI [auth b], UH [auth a], ZM [auth w]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	CJ [auth c], DD [auth D], EC [auth B], HC [auth C], OG [auth W], PJ [auth d], QI [auth b], WC [auth C], YM [auth w], ZI [auth c]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	FB [auth A], KD [auth D], OH [auth a], SJ [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	AN [auth y], GD [auth D], GF [auth R], HD [auth D], JD [auth D], KE [auth L], LE [auth N], MG [auth S], MJ [auth d], OM [auth s], TJ [auth d], UJ [auth d], UK [auth l], VG [auth Y], VK [auth n], XJ [auth g], YD [auth G], ZL [auth r]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	MD [auth E], WJ [auth e]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NEX	AG [auth S], BE [auth G], CK [auth g], GN [auth y], HL [auth n], HM [auth s], IF [auth R], ME [auth N], PL [auth r], TG [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
XAT	FK [auth g], GE [auth G], HF [auth R], KL [auth n], QK [auth g], RL [auth r], WD [auth G], ZE [auth N]	(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
LUT	BG [auth S], CE [auth G], EH [auth Y], GK [auth g], IL [auth n], KN [auth y], LL [auth n], MK [auth g], NM [auth s], OF [auth R], PE [auth N], RM [auth s], RN [auth y], UD [auth G], UL [auth r], WF [auth S], YE [auth N], YG [auth Y]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR	BC [auth B], BJ [auth c], DB [auth A], ED [auth D], GC [auth C], HE [auth H], IE [auth J], JE [auth K], JI [auth b], LH [auth a], LJ [auth d], NG [auth T], NI [auth b], QB [auth B], RK [auth h], SC [auth C], SK [auth j], TK [auth k], WB [auth B], XH [auth b], XI [auth c], XM [auth t]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BD [auth D], QJ [auth d]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX (Subject of Investigation/LOI)	FC [auth C], PH [auth a]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	IB [auth A], MH [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)	GB [auth A], TH [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	IH [auth a], NH [auth a], YA [auth A], ZA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Forsman, J.A., Graca, A.T., Hussein, R., Hall, M., Messinger, J., Schroder, W.P., Aydin, A.O.

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Funding Organization	Location	Grant Number
Sven och Lilly Lawskis fond for naturvetenskaplig forskning	Sweden	--
Swedish Research Council	Sweden	2020-03809
Carl Trygger Foundation	Sweden	CTS 19.324
Kempe Foundation	Sweden	JCK-2030
German Research Foundation (DFG)	Germany	TP A5

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release