9G6H | pdb_00009g6h

active PSII dimer from native Peak4 PSII dimers

• PDB DOI: https://doi.org/10.2210/pdb9G6H/pdb
• EM Map EMD-51102: 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

active PSII dimer from native Peak4 PSII dimers

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 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 38-mer - A10B4C4D2E2F2G2H2I2J2K2L2M2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 765.46 kDa 
• Atom Count: 51,092 
• Modeled Residue Count: 5,239 
• Deposited Residue Count: 5,650 
• Unique protein chains: 19

Macromolecules

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

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	FA [auth o], 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	GA [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	HA [auth u], 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	IA [auth v], 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	JA [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	KA [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	LA [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

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	AA [auth i], H [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