9M5A | pdb_00009m5a

cryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structure of photosystem II D1-V185T mutant from Thermosynechococcus vestitus

Shen, J.R.Jian, H.W.Nakajima, Y.Akita, F.Li, H.J.Kato, K.Sugiura, M.

(2026) Biochim Biophys Acta Bioenerg 

Macromolecule Content 

  • Total Structure Weight: 744.19 kDa 
  • Atom Count: 50,208 
  • Modeled Residue Count: 5,180 
  • Deposited Residue Count: 5,650 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 3A,
Q [auth a]
360Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for Q8DIV4 (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 betaE [auth F],
U [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: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HF [auth H],
V [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: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IG [auth I],
W [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: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JH [auth J],
X [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: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
Y [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: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
Z [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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MAA [auth m],
K [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: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBA [auth t],
L [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: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein UCA [auth u],
M [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: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein VDA [auth v],
N [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: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XEA [auth x],
O [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: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30FA [auth y],
P [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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UniProt GroupQ8DJI1
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaGA [auth E],
JA [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: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein OHA [auth O],
KA [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: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZIA [auth Z],
LA [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 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
AG [auth c]
ID [auth H]
MC [auth C]
NC [auth C]
OC [auth C]
AG [auth c],
ID [auth H],
MC [auth C],
NC [auth C],
OC [auth C],
UG [auth h],
YF [auth c],
ZF [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth C]
AF [auth b]
BB [auth B]
BC [auth C]
AB [auth B],
AC [auth C],
AF [auth b],
BB [auth B],
BC [auth C],
BF [auth b],
CB [auth B],
CC [auth C],
DB [auth B],
DC [auth C],
DE [auth a],
EB [auth B],
EC [auth C],
EE [auth a],
EG [auth d],
FB [auth B],
FC [auth C],
GB [auth B],
GC [auth C],
GE [auth a],
HB [auth B],
HC [auth C],
HG [auth d],
IB [auth B],
IC [auth C],
IG [auth d],
JB [auth B],
JC [auth C],
JF [auth c],
KB [auth B],
KF [auth c],
LB [auth B],
LF [auth c],
MB [auth B],
ME [auth b],
MF [auth c],
NB [auth B],
NE [auth b],
NF [auth c],
OB [auth B],
OE [auth b],
OF [auth c],
PE [auth b],
PF [auth c],
QA [auth A],
QE [auth b],
QF [auth c],
RA [auth A],
RE [auth b],
RF [auth c],
SC [auth D],
SE [auth b],
SF [auth c],
TA [auth A],
TE [auth b],
TF [auth c],
UE [auth b],
UF [auth c],
VC [auth D],
VE [auth b],
VF [auth c],
WC [auth D],
WE [auth b],
XB [auth C],
XE [auth b],
YB [auth C],
YE [auth b],
ZA [auth B],
ZB [auth C],
ZE [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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DG [auth d],
FE [auth a],
RC [auth D],
SA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



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DH [auth t]
FD [auth D]
IF [auth c]
KE [auth a]
RG [auth d]
DH [auth t],
FD [auth D],
IF [auth c],
KE [auth a],
RG [auth d],
TD [auth T],
WB [auth C],
XA [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



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BG [auth c]
CD [auth D]
CG [auth c]
FF [auth b]
IE [auth a]
BG [auth c],
CD [auth D],
CG [auth c],
FF [auth b],
IE [auth a],
OG [auth d],
PC [auth C],
QC [auth C],
SB [auth B],
VA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



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JE [auth a],
KG [auth d],
WA [auth A],
YC [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



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AD [auth D]
BD [auth D]
BH [auth l]
KH [auth E]
LG [auth d]
AD [auth D],
BD [auth D],
BH [auth l],
KH [auth E],
LG [auth d],
MG [auth d],
NG [auth d],
NH [auth e],
PD [auth L],
ZC [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



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HH [auth v],
WD [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



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GD [auth F],
SG [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX

Query on RRX



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HD [auth H],
TG [auth h]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



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AH [auth k]
CF [auth b]
DF [auth b]
EF [auth b]
FH [auth t]
AH [auth k],
CF [auth b],
DF [auth b],
EF [auth b],
FH [auth t],
HE [auth a],
JG [auth d],
JH [auth y],
KC [auth C],
LC [auth C],
OD [auth K],
PB [auth B],
QB [auth B],
RB [auth B],
RD [auth T],
UA [auth A],
WF [auth c],
XC [auth D],
XF [auth c],
YD [auth Y]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
CH [auth m]
EH [auth t]
GF [auth b]
MD [auth J]
QD [auth M]
CH [auth m],
EH [auth t],
GF [auth b],
MD [auth J],
QD [auth M],
TB [auth B],
UD [auth T],
VB [auth B],
VD [auth T],
YG [auth j]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
MA [auth A],
ZD [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
GG [auth d],
UC [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



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

Query on CA



Download:Ideal Coordinates CCD File
MH [auth O],
PH [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BE [auth a],
CE [auth a],
OA [auth A],
PA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
LD [auth J],
XG [auth j]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
DD [auth D]
ED [auth D]
FG [auth d]
GH [auth t]
HF [auth b]
DD [auth D],
ED [auth D],
FG [auth d],
GH [auth t],
HF [auth b],
IH [auth x],
JD [auth I],
KD [auth I],
LE [auth a],
LH [auth E],
ND [auth K],
OH [auth e],
PG [auth d],
QG [auth d],
SD [auth T],
TC [auth D],
UB [auth B],
VG [auth i],
WG [auth i],
XD [auth X],
YA [auth A],
ZG [auth k]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
G [auth I],
W [auth i]
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release