9G6G | pdb_00009g6g

Semi-active PSII dimer from native Peak4 PSII dimers

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G6G

This is version 1.0 of the entry. See complete history. 

Literature

Semi-active PSII dimer from the Peak4 PSII dimers

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

To be published.

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

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1360Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O]272Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TFA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U]134Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V]163Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinGA [auth x],
Q [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12HA [auth y],
R [auth Y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZIA [auth z],
S [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1T [auth a]360Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
GE [auth H]
IC [auth C]
JC [auth C]
JH [auth c]
KC [auth C]
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

Query on CLA


Download:Ideal Coordinates CCD File
AG [auth b]
AH [auth c]
BB [auth B]
BG [auth b]
BH [auth c]
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

Query on PHO


Download:Ideal Coordinates CCD File
EF [auth a],
HD [auth D],
PA [auth A],
TH [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
EC [auth B]
FE [auth F]
HF [auth a]
KF [auth a]
QD [auth D]
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

Query on LMG


Download:Ideal Coordinates CCD File
AJ [auth y]
CI [auth d]
ED [auth C]
IF [auth a]
LE [auth I]
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

Query on PL9


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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

Query on LHG


Download:Ideal Coordinates CCD File
AI [auth d]
BI [auth d]
MD [auth D]
ND [auth D]
OD [auth D]
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

Query on HEM


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CE [auth E],
II [auth f],
YE [auth V]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX


Download:Ideal Coordinates CCD File
HE [auth H],
ZI [auth x]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR


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AF [auth Y]
BJ [auth z]
FC [auth B]
GC [auth C]
GD [auth C]
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

Query on LMT


Download:Ideal Coordinates CCD File
AC [auth B]
CJ [auth z]
DE [auth E]
FD [auth C]
JI [auth f]
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

Query on OEX


Download:Ideal Coordinates CCD File
WA [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
LFA

Query on LFA


Download:Ideal Coordinates CCD File
AD [auth C]
BC [auth B]
BE [auth E]
CD [auth C]
DC [auth B]
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

Query on PLM


Download:Ideal Coordinates CCD File
AB [auth A]
AE [auth E]
BD [auth C]
CC [auth B]
DD [auth C]
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

Query on GOL


Download:Ideal Coordinates CCD File
VB [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
PF [auth a],
ZA [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
JA [auth A],
OF [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
UE [auth O]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
BF [auth a],
KA [auth A],
LA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME		AA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
HSK
Query on HSK		T [auth a]L-PEPTIDE LINKINGC6 H9 N3 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_4933+SVN

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/I00937X/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V002007/1

Revision History  (Full details and data files)

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