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- PDB-9wfz: Cryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus ve... -

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Basic information

Entry
Database: PDB / ID: 9wfz
TitleCryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus vestitus BP-1 (local refinement)
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
KeywordsPHOTOSYNTHESIS / PSII mutation / local refinement
Function / homology
Function and homology information


oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem II oxygen evolving complex / photosystem II assembly / response to herbicide / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II ...oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem II oxygen evolving complex / photosystem II assembly / response to herbicide / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ ...Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II protein D1 3 / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsFan, S.B. / Nakajima, Y. / Shen, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Structural and functional analysis of a photosystem II mutant PsbA3-S264V.
Authors: Songbo Fan / Yoshiki Nakajima / Koji Kato / Haowei Jiang / Pi-Cheng Tsai / Anqi Jia / Miwa Sugiura / Jian-Ren Shen /
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 ...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-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-binding region. Due to change of Ser to Val, the hydrogen-bond between the Q carbonyl oxygen and S264 is altered, which changed the protonation pathway of Q from the original route of D1-H252 through D1-S264 to Q, to a new, longer and less efficient route of D1-H252 through D1-F265 to Q. 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 and may function to transport protons to protonate Q. 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 protonation and function, as well as in the DCMU-binding.
History
DepositionAug 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
T: Photosystem II reaction center protein T
V: Photosystem II extrinsic protein V
Y: Photosystem II reaction center protein Psb30
A: Photosystem II protein D1 3
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
J: Photosystem II reaction center protein J
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II extrinsic protein O
U: Photosystem II extrinsic protein U
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
b: Photosystem II CP47 reaction center protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,82983
Polymers361,97619
Non-polymers41,85364
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 16 types, 17 molecules IKTVYABbCDJLMOUXZ

#1: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJZ6
#2: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5028.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1K9
#3: Protein/peptide Photosystem II reaction center protein T / PSII-T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ0
#4: Protein Photosystem II extrinsic protein V / PsbV / Cytochrome c-549 / Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A386
#5: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 5039.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJI1
#6: Protein Photosystem II protein D1 3 / PSII D1 protein 3 / Photosystem II Q(B) protein 3


Mass: 39792.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIV4, photosystem II
#7: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ1
#8: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50287.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIF8
#9: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem II Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8CM25, photosystem II
#12: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4105.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P59087
#13: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4299.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN8
#14: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3981.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHA7
#15: Protein Photosystem II extrinsic protein O / PsbO / Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 29637.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A431
#16: Protein Photosystem II extrinsic protein U / PSII-U / PsbU / Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein


Mass: 15030.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein X


Mass: 4322.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1R6
#18: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHJ2

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Cytochrome b559 subunit ... , 2 types, 2 molecules EF

#10: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9580.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIP0
#11: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN9

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Sugars , 2 types, 7 molecules

#21: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#33: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 497 molecules

#19: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#20: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#23: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CaMn4O5
#24: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#25: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#26: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#28: Chemical ChemComp-PL9 / 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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#29: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#30: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#31: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#34: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#35: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of PSII PsbA3-S264V from Thermosynechococcus vestitus BP-1 (local refinement)
Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93573 / Symmetry type: POINT

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