9G6F | pdb_00009g6f

Inactive PSII dimer from native Peak4 PSII dimers

• PDB DOI: https://doi.org/10.2210/pdb9G6F/pdb
• EM Map EMD-51100: 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 Model: experimental

Literature

Inactive PSII dimer from the Peak4 PSII pool

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 32-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 32-mer - A8B6C4D2E2F2G2H2I2J2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 632.24 kDa 
• Atom Count: 42,670 
• Modeled Residue Count: 4,211 
• Deposited Residue Count: 4,512 
• Unique protein chains: 16

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1 1	A, Q [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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B, R [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, S [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, T [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, U [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, V [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], W [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	H [auth I], X [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	I [auth J], Y [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	J [auth K], Z [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	AA [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	BA [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 reaction center protein T	CA [auth t], M [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: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	DA [auth x], N [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: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	EA [auth y], O [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: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	FA [auth z], P [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

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	JD [auth D], LH [auth d], PD [auth H], QC [auth C], QH [auth h], TG [auth c], UG [auth c], WD [auth J], WG [auth c]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AB [auth B], AF [auth b], BB [auth B], BF [auth b], BH [auth d], CB [auth B], CC [auth C], CD [auth D], CF [auth b], CH [auth d], DB [auth B], DC [auth C], DD [auth D], DF [auth b], EB [auth B], EC [auth C], EF [auth b], FB [auth B], FC [auth C], FF [auth b], FG [auth c], GB [auth B], GC [auth C], GF [auth b], GG [auth c], HB [auth B], HC [auth C], HF [auth b], HG [auth c], IA [auth A], IB [auth B], IC [auth C], IF [auth b], IG [auth c], JA [auth A], JB [auth B], JC [auth C], JF [auth b], JG [auth c], KA [auth A], KB [auth B], KC [auth C], KF [auth b], KG [auth c], LB [auth B], LC [auth C], LE [auth a], LF [auth b], LG [auth c], MA [auth A], MB [auth B], MC [auth C], ME [auth a], MF [auth b], MG [auth c], NC [auth C], NE [auth a], NF [auth b], NG [auth c], OC [auth C], OF [auth b], OG [auth c], PE [auth a], PF [auth b], PG [auth c], QG [auth c], RG [auth c], XA [auth B], YA [auth B], ZA [auth B]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	LA [auth A], OE [auth a], VC [auth D], ZG [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	BE [auth L], BI [auth l], MD [auth F], OA [auth A], OH [auth f], QA [auth A], RE [auth a], TE [auth a]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AC [auth C], EG [auth c], HH [auth d], ID [auth D], QB [auth B], RC [auth C], TF [auth b], VG [auth c]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	EH [auth d], FD [auth D], PA [auth A], SE [auth a]	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	AE [auth L], AI [auth l], FH [auth d], GD [auth D], GH [auth d], HD [auth D], WA [auth A], WE [auth a], XE [auth a]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	LD [auth F], NH [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
RRX	HI [auth x], OD [auth H]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	DH [auth d], ED [auth D], GE [auth Y], II [auth y], NA [auth A], NB [auth B], OB [auth B], PB [auth B], PC [auth C], QE [auth a], QF [auth b], RF [auth b], SF [auth b], SG [auth c], UC [auth C], XG [auth c], YD [auth K], YE [auth b], YH [auth k], ZB [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BC [auth C], CE [auth M], CI [auth m], DE [auth M], DI [auth m], FI [auth t], JH [auth d], JI [auth z], VH [auth i], WC [auth D], XC [auth D], YG [auth d], ZE [auth b]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
LFA	AD [auth D], AG [auth b], BD [auth D], DG [auth b], EE [auth M], EI [auth m], FE [auth X], GI [auth x], HE [auth Z], IH [auth d], KH [auth d], ND [auth H], PH [auth h], QD [auth H], RA [auth A], RB [auth B], RH [auth h], SC [auth C], SH [auth h], TA [auth A], UB [auth B], UD [auth I], UE [auth a], VB [auth B], VF [auth b], XD [auth J], XF [auth b], XH [auth i], YB [auth B], YC [auth D], YF [auth b], ZD [auth K], ZH [auth k]	EICOSANE C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N
PLM	BG [auth b], CG [auth b], IE [auth a], KD [auth E], MH [auth e], RD [auth H], SA [auth A], SB [auth B], SD [auth I], TB [auth B], TC [auth C], TD [auth I], TH [auth i], UA [auth A], UF [auth b], UH [auth i], VD [auth I], VE [auth a], WB [auth B], WF [auth b], WH [auth i], XB [auth B], ZC [auth D], ZF [auth b]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
BCT	AH [auth d], VA [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	GA [auth A], JE [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	HA [auth A], KE [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

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
RECONSTRUCTION	RELION	4.0.0
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