Skip to main content

 9WFZ | pdb_00009wfz

Cryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus vestitus BP-1 (local refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9WFZ

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

Literature

Structural and functional analysis of a photosystem II mutant PsbA3-S264V.

Fan, S., Nakajima, Y., Kato, K., Jiang, H., Tsai, P.C., Jia, A., Sugiura, M., Shen, J.R.

(2026) Biochim Biophys Acta Bioenerg 1868: 149607-149607

  • DOI: https://doi.org/10.1016/j.bbabio.2026.149607
  • Primary Citation Related Structures: 
    9W5B, 9W7D, 9WFZ

  • PubMed Abstract: 

    Photosystem II (PSII) catalyzes water oxidation and oxygen evolution by a light-induced electron transfer chain, leading to the generation of electrons, protons and dioxygen. D1-S264 is a residue located close to the Q B -binding site, and mutation of this residue has been shown to bring significant effects on the electron transfer and oxygen-evolving activities. Here we analyzed the structure of a Thermosynechococcus elongatus mutant PsbA3-S264V by cryo-electron microscopy at 1.96 Å resolution, which showed significant changes in the structure surrounding the bicarbonate and Q B -binding region. Due to change of Ser to Val, the hydrogen-bond between the Q B carbonyl oxygen and S264 is altered, which changed the protonation pathway of Q B from the original route of D1-H252 through D1-S264 to Q B , to a new, longer and less efficient route of D1-H252 through D1-F265 to Q B . Two residues, D1-E244 and D2-E242, changed their side chain orientations significantly. Among them, D2-E242 adopted two conformations, and both are largely deviated from the original structure. All these changes led to alterations in hydrogen-bonding networks of two channels, channel A and channel B, that connect the stromal surface to Q B and may function to transport protons to protonate Q B . Furthermore, isothermal titration calorimetry experiments showed a diminished 3-(3,4-dichlorophenyl)-1, 1-dimethylurea (DCMU) binding affinity of the mutated PSII, which may be explained by a structural rotation of D1-F255 in the mutant based on structural analysis of DCMU-bound PSII. These findings offer valuable insights into the functions of D1-S264 in Q B protonation and function, as well as in the DCMU-binding.


  • Organizational Affiliation: 
    • Advanced Research Field, Research Institute for Interdisciplinary Science, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan.

Macromolecule Content 

  • Total Structure Weight: 403.83 kDa 
  • Atom Count: 17,446 
  • Modeled Residue Count: 2,046 
  • Deposited Residue Count: 3,269 
  • Unique protein chains: 18

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IA [auth I]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJZ6 
Go to UniProtKB:  Q8DJZ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJZ6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KB [auth K]46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1K9 
Go to UniProtKB:  Q9F1K9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1K9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TC [auth T]32Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIQ0 
Go to UniProtKB:  Q8DIQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIQ0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein VD [auth V]163Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A386 
Go to UniProtKB:  P0A386
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A386
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30E [auth Y]46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJI1 
Go to UniProtKB:  Q8DJI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJI1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 3F [auth A]360Thermosynechococcus vestitus BP-1Mutation(s): 1 
EC: 1.10.3.9
UniProt
Find proteins for Q8DIV4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIV4 
Go to UniProtKB:  Q8DIV4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIV4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinG [auth B],
S [auth b]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIQ1 
Go to UniProtKB:  Q8DIQ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIQ1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinH [auth C]461Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIF8 
Go to UniProtKB:  Q8DIF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIF8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinI [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))
Explore Q8CM25 
Go to UniProtKB:  Q8CM25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CM25
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaJ [auth E]84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIP0 
Go to UniProtKB:  Q8DIP0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIP0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaK [auth F]45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIN9 
Go to UniProtKB:  Q8DIN9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIN9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JL [auth J]40Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P59087 
Go to UniProtKB:  P59087
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59087
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LM [auth L]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DIN8 
Go to UniProtKB:  Q8DIN8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DIN8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MN [auth M]36Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DHA7 
Go to UniProtKB:  Q8DHA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DHA7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein O272Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A431 
Go to UniProtKB:  P0A431
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A431
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II extrinsic protein UP [auth U]134Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q9F1L5 
Go to UniProtKB:  Q9F1L5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1L5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XQ [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 
Go to UniProtKB:  Q9F1R6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F1R6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZR [auth Z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DHJ2 
Go to UniProtKB:  Q8DHJ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DHJ2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on DGD



Download:Ideal Coordinates CCD File
IB [auth C],
JB [auth C],
KB [auth C],
YB [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EB [auth C]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HA [auth A],
HB [auth C],
IA [auth A],
KA [auth A],
LB [auth C],
NB [auth D],
OA [auth A],
OB [auth D],
PB [auth D],
QB [auth D],
RB [auth D],
TA [auth B],
UA [auth B],
YA [auth C],
ZA [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
JA [auth A],
MB [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
AC [auth F],
WA [auth C]
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
VA [auth B],
VB [auth D],
XA [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
MA [auth A],
TB [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
CC [auth L],
QA [auth A],
RA [auth A],
UB [auth D],
XB [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
CA [auth V]HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM



Download:Ideal Coordinates CCD File
ZB [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AA [auth T]
LA [auth A]
SA [auth A]
SB [auth D]
U [auth I]
AA [auth T],
LA [auth A],
SA [auth A],
SB [auth D],
U [auth I],
V [auth K],
W [auth K],
Y [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BA [auth T],
BC [auth J],
DC [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX



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

Query on BCT



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

Query on FE2



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

Query on CL



Download:Ideal Coordinates CCD File
FA [auth A],
GA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL

Query on UNL



Download:Ideal Coordinates CCD File
EC [auth X]
NA [auth A]
T [auth I]
WB [auth D]
X [auth K]
EC [auth X],
NA [auth A],
T [auth I],
WB [auth D],
X [auth K],
Z [auth T]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

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: 2026-09-23
    Type: Initial release