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- PDB-9t5u: Chlorophyll f-containing monomeric far-red Photosystem II from Ca... -

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Basic information

Entry
Database: PDB / ID: 9t5u
TitleChlorophyll f-containing monomeric far-red Photosystem II from Calothrix sp. NIES-3974
Components
  • PsbA
  • PsbB
  • PsbC
  • PsbD
  • PsbE
  • PsbF
  • PsbH
  • PsbI
  • PsbJ
  • PsbK
  • PsbL
  • PsbM
  • PsbT
  • PsbX
  • PsbY
  • PsbZ
  • Ycf12
KeywordsELECTRON TRANSPORT / Chlorophyll f / photosystem II / FaRLiP
Function / homology
Function and homology information


BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD
Similarity search - Component
Biological speciesCalothrix sp. NIES-3974 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsLeong, H.F. / Consoli, G. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W.
Funding support United Kingdom, European Union, 11items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X019284/1 United Kingdom
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Royal SocietyRSRP/S2/242010 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z516740/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)UKRI2820 United Kingdom
Imperial College LondonPresidents PhD Scholarship United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Mapping the absorption landscape of far-red Photosystem II
Authors: Leong, H.F. / Consoli, G. / Davis, G.A. / Hancox-Lachman, B. / Renard, K. / Tufail, F. / Lee, L.E. / Gautier, L. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W.
History
DepositionNov 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PsbA
B: PsbB
C: PsbC
D: PsbD
E: PsbE
F: PsbF
H: PsbH
I: PsbI
J: PsbJ
K: PsbK
L: PsbL
M: PsbM
R: PsbY
T: PsbT
X: PsbX
Y: Ycf12
Z: PsbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,68597
Polymers255,92417
Non-polymers60,76180
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 7 molecules ABCDEHZ

#1: Protein PsbA


Mass: 40209.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#2: Protein PsbB


Mass: 56801.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#3: Protein PsbC


Mass: 50618.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#4: Protein PsbD


Mass: 39942.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#5: Protein PsbE


Mass: 9382.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#7: Protein PsbH


Mass: 7636.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#17: Protein PsbZ


Mass: 6740.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)

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Protein/peptide , 10 types, 10 molecules FIJKLMRTXY

#6: Protein/peptide PsbF


Mass: 5224.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#8: Protein/peptide PsbI


Mass: 4367.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#9: Protein/peptide PsbJ


Mass: 3872.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#10: Protein/peptide PsbK


Mass: 5062.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#11: Protein/peptide PsbL


Mass: 4546.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#12: Protein/peptide PsbM


Mass: 4299.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#13: Protein/peptide PsbY


Mass: 4444.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#14: Protein/peptide PsbT


Mass: 3973.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#15: Protein/peptide PsbX


Mass: 4381.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)
#16: Protein/peptide Ycf12


Mass: 4421.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Calothrix sp. NIES-3974 (bacteria)

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Sugars , 2 types, 9 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#31: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 188 molecules

#18: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H70MgN4O6
#23: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#24: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56
#25: 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.: 3 / Source method: obtained synthetically / Formula: C41H78O12S
#26: 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
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#29: Chemical ChemComp-F6C / Chlorophyll F / [methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium


Mass: 905.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#33: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Chlorophyll f-containing monomeric far-red Photosystem II
Type: COMPLEX
Details: Chlorophyll f-containing monomeric far-red Photosystem II from Calothrix sp. NIES-3974
Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Calothrix sp. NIES-3974 (bacteria)
Buffer solutionpH: 6.5
Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.8 adjusted with NaOH
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285844 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 91.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006922232
ELECTRON MICROSCOPYf_angle_d0.832230523
ELECTRON MICROSCOPYf_chiral_restr0.04083007
ELECTRON MICROSCOPYf_plane_restr0.00763689
ELECTRON MICROSCOPYf_dihedral_angle_d12.90129114

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