9G6G | pdb_00009g6g

Semi-active PSII dimer from native Peak4 PSII dimers

• PDB DOI: https://doi.org/10.2210/pdb9G6G/pdb
• EM Map EMD-51101: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Thermosynechococcus vestitus BP-1
• Mutation(s): No 


• Deposited: 2024-07-18 Released: 2025-07-30 
• Deposition Author(s): Zhao, Z., Vercellino, I., Nixon, P.J., Sazanov, L.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Semi-active PSII dimer from the Peak4 PSII dimers

Zhao, Z., Vercellino, I., Nixon, P.J., Sazanov, L.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 35-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q1R1S1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 35-mer - A13B4C3D2E2F2G2H2I2J1K1L1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 32-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 32-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 702.58 kDa 
• Atom Count: 47,004 
• Modeled Residue Count: 4,727 
• Deposited Residue Count: 5,081 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1 1	A	360	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A444  Go to UniProtKB:  P0A444

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, U [auth b]	510	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ1  Go to UniProtKB:  Q8DIQ1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C, V [auth c]	461	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIF8  Go to UniProtKB:  Q8DIF8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, W [auth d]	352	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.10.3.9
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8CM25  Go to UniProtKB:  Q8CM25

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, X [auth e]	84	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIP0  Go to UniProtKB:  Q8DIP0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Y [auth f]	45	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN9  Go to UniProtKB:  Q8DIN9

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth H], Z [auth h]	66	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJ43  Go to UniProtKB:  Q8DJ43

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	AA [auth i], H [auth I]	38	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJZ6  Go to UniProtKB:  Q8DJZ6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	BA [auth j], I [auth J]	40	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P59087  Go to UniProtKB:  P59087

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	CA [auth k], J [auth K]	46	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1K9  Go to UniProtKB:  Q9F1K9

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	DA [auth l], K [auth L]	37	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN8  Go to UniProtKB:  Q8DIN8

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	EA [auth m], L [auth M]	36	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHA7  Go to UniProtKB:  Q8DHA7

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	M [auth O]	272	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A431  Go to UniProtKB:  P0A431

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	FA [auth t], N [auth T]	32	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ0  Go to UniProtKB:  Q8DIQ0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	O [auth U]	134	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1L5  Go to UniProtKB:  Q9F1L5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	P [auth V]	163	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A386  Go to UniProtKB:  P0A386

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	GA [auth x], Q [auth X]	41	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1R6  Go to UniProtKB:  Q9F1R6

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	HA [auth y], R [auth Y]	46	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJI1  Go to UniProtKB:  Q8DJI1

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	IA [auth z], S [auth Z]	62	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHJ2  Go to UniProtKB:  Q8DHJ2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1 1	T [auth a]	360	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A444  Go to UniProtKB:  P0A444

Small Molecules

Ligands 19 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	GE [auth H], IC [auth C], JC [auth C], JH [auth c], KC [auth C], KH [auth c], LH [auth c], LI [auth h], RD [auth D], YH [auth d]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AG [auth b], AH [auth c], BB [auth B], BG [auth b], BH [auth c], CB [auth B], CF [auth a], CG [auth b], CH [auth c], DB [auth B], DF [auth a], DG [auth b], DH [auth c], EB [auth B], EG [auth b], EH [auth c], FB [auth B], FF [auth a], FG [auth b], FH [auth c], GB [auth B], GG [auth b], GH [auth c], HB [auth B], HG [auth b], HH [auth c], IB [auth B], IG [auth b], IH [auth c], JB [auth B], JG [auth b], KB [auth B], KD [auth D], KG [auth b], LB [auth B], LC [auth C], LD [auth D], MA [auth A], MB [auth B], MC [auth C], NA [auth A], NB [auth B], NC [auth C], OA [auth A], OB [auth B], OC [auth C], PB [auth B], PC [auth C], QA [auth A], QB [auth B], QC [auth C], RC [auth C], SC [auth C], SH [auth d], TC [auth C], UC [auth C], VC [auth C], VF [auth b], VH [auth d], WC [auth C], WF [auth b], WG [auth c], WH [auth d], XC [auth C], XF [auth b], XG [auth c], YF [auth b], YG [auth c], ZF [auth b], ZG [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	EF [auth a], HD [auth D], PA [auth A], TH [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	EC [auth B], FE [auth F], HF [auth a], KF [auth a], QD [auth D], TA [auth A], UF [auth b], XA [auth A], ZH [auth d]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AJ [auth y], CI [auth d], ED [auth C], IF [auth a], LE [auth I], OG [auth b], PD [auth D], QH [auth c], TB [auth B], ZE [auth Y]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	ID [auth D], JF [auth a], SA [auth A], XH [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	AI [auth d], BI [auth d], MD [auth D], ND [auth D], OD [auth D], QF [auth a], RE [auth L], RF [auth a], VI [auth l], YD [auth E]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	CE [auth E], II [auth f], YE [auth V]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
RRX	HE [auth H], ZI [auth x]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	AF [auth Y], BJ [auth z], FC [auth B], GC [auth C], GD [auth C], GF [auth a], HC [auth C], HI [auth f], JD [auth D], LG [auth b], MG [auth b], NG [auth b], PI [auth i], RA [auth A], RB [auth B], RI [auth j], SB [auth B], SI [auth k], VE [auth T], XI [auth t]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	AC [auth B], CJ [auth z], DE [auth E], FD [auth C], JI [auth f], LF [auth a], MH [auth c], OE [auth J], SE [auth M], TE [auth M], TF [auth a], UB [auth B], UH [auth d], WE [auth T], XD [auth D], XE [auth T], YA [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX	WA [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
LFA	AD [auth C], BC [auth B], BE [auth E], CD [auth C], DC [auth B], DI [auth d], FI [auth d], GI [auth e], IE [auth H], JE [auth I], KE [auth I], KI [auth h], ME [auth I], MF [auth a], NE [auth I], QI [auth i], RG [auth b], SD [auth D], SF [auth a], SG [auth b], TD [auth D], UA [auth A], UG [auth b], VA [auth A], WB [auth B], WD [auth D], WI [auth m], XB [auth B], ZB [auth B], ZC [auth C]	EICOSANE C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N
PLM	AB [auth A], AE [auth E], BD [auth C], CC [auth B], DD [auth C], EE [auth E], EI [auth d], MI [auth h], NF [auth a], NH [auth c], NI [auth i], OH [auth c], OI [auth i], PE [auth J], PG [auth b], PH [auth c], QE [auth K], QG [auth b], RH [auth c], TG [auth b], TI [auth k], UD [auth D], UI [auth l], VD [auth D], VG [auth b], YB [auth B], YC [auth C], YI [auth x], ZD [auth E]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
GOL	VB [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	PF [auth a], ZA [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	JA [auth A], OF [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	UE [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	BF [auth a], KA [auth A], LA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	AA [auth i], H [auth I]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET
HSK	T [auth a]	L-PEPTIDE LINKING	C6 H9 N3 O3		HIS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_4933+SVN

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Zhao, Z., Vercellino, I., Nixon, P.J., Sazanov, L.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/I00937X/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V002007/1

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release