9G6F | pdb_00009g6f

Inactive 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 Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G6F

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

Literature

Inactive PSII dimer from the Peak4 PSII pool

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

To be published.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
Q [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
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
R [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,
S [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,
T [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,
U [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,
V [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],
W [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 IH [auth I],
X [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 JI [auth J],
Y [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 KJ [auth K],
Z [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 LAA [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 MBA [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 reaction center protein TCA [auth t],
M [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: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinDA [auth x],
N [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1R6 
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UniProt GroupQ9F1R6
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12EA [auth y],
O [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: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZFA [auth z],
P [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

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
JD [auth D]
LH [auth d]
PD [auth H]
QC [auth C]
QH [auth h]
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

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth B]
AF [auth b]
BB [auth B]
BF [auth b]
BH [auth d]
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

Query on PHO


Download:Ideal Coordinates CCD File
LA [auth A],
OE [auth a],
VC [auth D],
ZG [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
BE [auth L]
BI [auth l]
MD [auth F]
OA [auth A]
OH [auth f]
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

Query on LMG


Download:Ideal Coordinates CCD File
AC [auth C]
EG [auth c]
HH [auth d]
ID [auth D]
QB [auth B]
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

Query on PL9


Download:Ideal Coordinates CCD File
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

Query on LHG


Download:Ideal Coordinates CCD File
AE [auth L]
AI [auth l]
FH [auth d]
GD [auth D]
GH [auth d]
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

Query on HEM


Download:Ideal Coordinates CCD File
LD [auth F],
NH [auth f]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX


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

Query on BCR


Download:Ideal Coordinates CCD File
DH [auth d]
ED [auth D]
GE [auth Y]
II [auth y]
NA [auth A]
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

Query on LMT


Download:Ideal Coordinates CCD File
BC [auth C]
CE [auth M]
CI [auth m]
DE [auth M]
DI [auth m]
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

Query on LFA


Download:Ideal Coordinates CCD File
AD [auth D]
AG [auth b]
BD [auth D]
DG [auth b]
EE [auth M]
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

Query on PLM


Download:Ideal Coordinates CCD File
BG [auth b]
CG [auth b]
IE [auth a]
KD [auth E]
MH [auth e]
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

Query on BCT


Download:Ideal Coordinates CCD File
AH [auth d],
VA [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
GA [auth A],
JE [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL


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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.0
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