7YMI

PSII-Pcb Dimer of Acaryochloris Marina

• PDB DOI: https://doi.org/10.2210/pdb7YMI/pdb
• EM Map EMD-33929: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Acaryochloris marina MBIC11017
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2022-07-28 Released: 2023-08-16 
• Deposition Author(s): Shen, L.L., Gao, Y.Z., Wang, W.D., Zhang, X., Shen, J.R., Wang, P.Y., Han, G.Y.
• Funding Organization(s): Chinese Academy of Sciences, National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

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

Literature

Structure of a large photosystem II supercomplex from Acaryochloris marina.

Shen, L.L., Gao, Y.Z., Wang, W.D., Zhang, X., Shen, J.R., Wang, P.Y., Han, G.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 40-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 40-mer - A10B7C6D4E2F2G2H2I2J2K1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,079.02 kDa 
• Atom Count: 68,428 
• Modelled Residue Count: 6,692 
• Deposited Residue Count: 7,498 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1 2	A, U [auth a]	360	Acaryochloris marina MBIC11017	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A5A8K9 (Acaryochloris marina (strain MBIC 11017)) Explore A5A8K9  Go to UniProtKB:  A5A8K9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, V [auth b]	506	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0CFM2 (Acaryochloris marina (strain MBIC 11017)) Explore B0CFM2  Go to UniProtKB:  B0CFM2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C, W [auth c]	490	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C1V7 (Acaryochloris marina (strain MBIC 11017)) Explore B0C1V7  Go to UniProtKB:  B0C1V7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein 1	D, X [auth d]	351	Acaryochloris marina MBIC11017	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for B0C1V6 (Acaryochloris marina (strain MBIC 11017)) Explore B0C1V6  Go to UniProtKB:  B0C1V6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, Y [auth e]	83	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C6T2 (Acaryochloris marina (strain MBIC 11017)) Explore B0C6T2  Go to UniProtKB:  B0C6T2

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein Y	F, Z [auth f]	99	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C2V2 (Acaryochloris marina (strain MBIC 11017)) Explore B0C2V2  Go to UniProtKB:  B0C2V2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 10 kDa phosphoprotein PsbH	AA [auth h], G [auth H]	71	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0CDZ2 (Acaryochloris marina (strain MBIC 11017)) Explore B0CDZ2  Go to UniProtKB:  B0CDZ2

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein PsbI	BA [auth i], H [auth I]	34	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C5R5 (Acaryochloris marina (strain MBIC 11017)) Explore B0C5R5  Go to UniProtKB:  B0C5R5

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	CA [auth k], I [auth K]	45	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C6Z7 (Acaryochloris marina (strain MBIC 11017)) Explore B0C6Z7  Go to UniProtKB:  B0C6Z7

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	DA [auth l], J [auth L]	38	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C6T1 (Acaryochloris marina (strain MBIC 11017)) Explore B0C6T1  Go to UniProtKB:  B0C6T1

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	EA [auth m], K [auth M]	34	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0CFM0 (Acaryochloris marina (strain MBIC 11017)) Explore B0CFM0  Go to UniProtKB:  B0CFM0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	FA [auth t], L [auth T]	46	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C605 (Acaryochloris marina (strain MBIC 11017)) Explore B0C605  Go to UniProtKB:  B0C605

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	GA [auth x], M [auth X]	40	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0BYW9 (Acaryochloris marina (strain MBIC 11017)) Explore B0BYW9  Go to UniProtKB:  B0BYW9

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	HA [auth y], N [auth Y]	39	Acaryochloris marina MBIC11017	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	IA [auth z], O [auth Z]	62	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C0S7 (Acaryochloris marina (strain MBIC 11017)) Explore B0C0S7  Go to UniProtKB:  B0C0S7

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
High light inducible protein	JA [auth 6], P [auth 2]	352	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C3E5 (Acaryochloris marina (strain MBIC 11017)) Explore B0C3E5  Go to UniProtKB:  B0C3E5

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein	KA [auth g], Q [auth G]	41	Acaryochloris marina MBIC11017	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
High light inducible protein	LA [auth 5], R [auth 1]	356	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C576 (Acaryochloris marina (strain MBIC 11017)) Explore B0C576  Go to UniProtKB:  B0C576

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
High light inducible protein	MA [auth 7], S [auth 3]	349	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C6I0 (Acaryochloris marina (strain MBIC 11017)) Explore B0C6I0  Go to UniProtKB:  B0C6I0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
High light inducible protein	NA [auth 8], T [auth 4]	353	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C3E6 (Acaryochloris marina (strain MBIC 11017)) Explore B0C3E6  Go to UniProtKB:  B0C3E6

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD (Subject of Investigation/LOI)	MC [auth C], MI [auth c], SB [auth B], UH [auth b]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CL7 (Subject of Investigation/LOI)	AB [auth B], AC [auth C], AF [auth 3], AG [auth 4], AH [auth b], AI [auth c], AK [auth 5], AL [auth 7], AM [auth 8], BB [auth B], BC [auth C], BD [auth 2], BE [auth 1], BF [auth 3], BG [auth 4], BH [auth b], BI [auth c], BJ [auth 6], BK [auth 5], BL [auth 7], BM [auth 8], CB [auth B], CC [auth C], CD [auth 2], CE [auth 1], CF [auth 3], CG [auth 4], CH [auth b], CI [auth c], CJ [auth 6], CK [auth 5], CL [auth 7], CM [auth 8], DB [auth B], DC [auth C], DD [auth 2], DE [auth 1], DF [auth 3], DG [auth 4], DH [auth b], DI [auth c], DJ [auth 6], DK [auth 5], DL [auth 7], DM [auth 8], EB [auth B], EC [auth C], ED [auth 2], EE [auth 1], EF [auth 3], EG [auth 4], EH [auth b], EI [auth c], EJ [auth 6], EK [auth 5], EL [auth 7], EM [auth 8], FB [auth B], FC [auth C], FD [auth 2], FE [auth 1], FF [auth 3], FG [auth 4], FH [auth b], FI [auth c], FJ [auth 6], FK [auth 5], FL [auth 7], FM [auth 8], GB [auth B], GC [auth C], GD [auth 2], GE [auth 1], GF [auth 3], GG [auth 4], GH [auth b], GI [auth c], GJ [auth 6], GK [auth 5], GL [auth 7], GM [auth 8], HB [auth B], HC [auth C], HD [auth 2], HE [auth 1], HF [auth 3], HG [auth 4], HH [auth b], HI [auth c], HJ [auth 6], HK [auth 5], HL [auth 7], HM [auth 8], IB [auth B], IC [auth C], ID [auth 2], IE [auth 1], IF [auth 3], IG [auth 4], IH [auth b], II [auth c], IJ [auth 6], IK [auth 5], IL [auth 7], IM [auth 8], JB [auth B], JC [auth C], JD [auth 2], JE [auth 1], JF [auth 3], JG [auth 4], JH [auth b], JI [auth c], JJ [auth 6], JK [auth 5], JL [auth 7], JM [auth 8], KB [auth B], KD [auth 2], KE [auth 1], KF [auth 3], KG [auth 4], KH [auth b], KJ [auth 6], KK [auth 5], KL [auth 7], KM [auth 8], LD [auth 2], LE [auth 1], LF [auth 3], LG [auth 4], LH [auth b], LJ [auth 6], LK [auth 5], LL [auth 7], MD [auth 2], ME [auth 1], MF [auth 3], MG [auth 4], MH [auth b], MJ [auth 6], MK [auth 5], ML [auth 7], NC [auth C], ND [auth 2], NE [auth 1], NF [auth 3], NI [auth c], NJ [auth 6], NK [auth 5], NL [auth 7], OA [auth A], OD [auth 2], OE [auth 1], OF [auth 3], OJ [auth 6], OK [auth 5], PD [auth 2], PE [auth 1], PJ [auth 6], PK [auth 5], QA [auth A], QB [auth B], QC [auth D], QD [auth 2], QE [auth 1], QG [auth a], QI [auth d], QJ [auth 6], QK [auth 5], RD [auth 2], RE [auth 1], RJ [auth 6], RK [auth 5], SC [auth D], SD [auth 2], SE [auth 1], SG [auth a], SH [auth b], SI [auth d], SJ [auth 6], SK [auth 5], TA [auth A], TC [auth D], TE [auth 1], TI [auth d], UG [auth a], VA [auth B], WA [auth B], WK [auth 7], XA [auth B], XB [auth C], XE [auth 3], XG [auth b], XH [auth c], XK [auth 7], XL [auth 8], YA [auth B], YB [auth C], YE [auth 3], YG [auth b], YH [auth c], YK [auth 7], YL [auth 8], ZA [auth B], ZB [auth C], ZE [auth 3], ZF [auth 4], ZG [auth b], ZH [auth c], ZK [auth 7], ZL [auth 8]	CHLOROPHYLL D C54 H70 Mg N4 O6 FBCRYORFRGRJBC-ACDPFEIMSA-L
PHO (Subject of Investigation/LOI)	PA [auth A], RG [auth a], WC [auth D], WI [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)	OB [auth B], QH [auth b], QL [auth 7], RF [auth 3], SA [auth A], SL [auth 7], TF [auth 3], UB [auth B], VJ [auth 6], VK [auth 5], WD [auth 2], WE [auth 1], XJ [auth 6], YD [auth 2]	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)	AE [auth 1], PB [auth B], RH [auth b], WB [auth C], WH [auth c], YC [auth D], YI [auth d], ZJ [auth 5]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)	VC [auth D], VI [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)	RB [auth B], TB [auth B], TH [auth b], TL [auth 7], UA [auth A], UF [auth 3], UL [auth 8], VG [auth a], VH [auth b], WF [auth 4], XC [auth D], XI [auth d]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)	ZC [auth F], ZI [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZEX (Subject of Investigation/LOI)	LM [auth 8], MM [auth 8], NG [auth 4], NM [auth 8], OG [auth 4], OL [auth 7], PF [auth 3], PG [auth 4], PL [auth 7], QF [auth 3], RL [auth 7], SF [auth 3], TD [auth 2], TJ [auth 6], TK [auth 5], UD [auth 2], UE [auth 1], UJ [auth 6], UK [auth 5], VD [auth 2], VE [auth 1], VF [auth 3], WJ [auth 6], WL [auth 8], XD [auth 2], YF [auth 4], YJ [auth 6], ZD [auth 2]	(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol C40 H56 O2 YRMDXLDAZBQLBK-WIHRHFSMSA-N
8CT (Subject of Investigation/LOI)	AD [auth K], AJ [auth k], KC [auth C], KI [auth c], LB [auth B], LC [auth C], LI [auth c], MB [auth B], NB [auth B], NH [auth b], OC [auth C], OH [auth b], OI [auth c], PH [auth b], RA [auth A], TG [auth a], UC [auth D], UI [auth d], VB [auth B], VL [auth 8], WG [auth b], XF [auth 4]	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene C40 H56 ANVAOWXLWRTKGA-GZSHKXEASA-N
BCT (Subject of Investigation/LOI)	RC [auth D], RI [auth d]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)	PC [auth D], PI [auth d]	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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Shen, L.L., Gao, Y.Z., Wang, W.D., Zhang, X., Shen, J.R., Wang, P.Y., Han, G.Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	QYZDY-SSW-SMC003
Chinese Academy of Sciences	China	XDB17000000
National Basic Research Program of China (973 Program)	China	2015CB150100

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release