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- PDB-7f4v: Cryo-EM structure of a primordial cyanobacterial photosystem I -

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Basic information

Entry
Database: PDB / ID: 7f4v
TitleCryo-EM structure of a primordial cyanobacterial photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • Photosystem I iron-sulfur center
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily ...Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Menaquinone-4 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit Z / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 ...Menaquinone-4 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit Z / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsKato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Yonekura, K. / Shen, J.R.
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI
Authors: Kato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Ueno, Y. / Suzuki, T. / Uchida, H. / Murakami, A. / Nakajima, Y. / Yokono, M. / Akimoto, S. / Dohmae, N. / Yonekura, K. / Shen, J.R.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
aA: Photosystem I P700 chlorophyll a apoprotein A1
aB: Photosystem I P700 chlorophyll a apoprotein A2
aC: Photosystem I iron-sulfur center
aD: Photosystem I reaction center subunit II
aE: Photosystem I reaction center subunit IV
aF: Photosystem I reaction center subunit III
aI: Photosystem I reaction center subunit Z
aJ: Unknown protein
aL: Photosystem I reaction center subunit XI
aM: Photosystem I reaction center subunit XII
bA: Photosystem I P700 chlorophyll a apoprotein A1
bB: Photosystem I P700 chlorophyll a apoprotein A2
bC: Photosystem I iron-sulfur center
bD: Photosystem I reaction center subunit II
bE: Photosystem I reaction center subunit IV
bF: Photosystem I reaction center subunit III
bI: Photosystem I reaction center subunit Z
bJ: Unknown protein
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
cA: Photosystem I P700 chlorophyll a apoprotein A1
cB: Photosystem I P700 chlorophyll a apoprotein A2
cC: Photosystem I iron-sulfur center
cD: Photosystem I reaction center subunit II
cE: Photosystem I reaction center subunit IV
cF: Photosystem I reaction center subunit III
cI: Photosystem I reaction center subunit Z
cJ: Unknown protein
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,067,066384
Polymers781,59130
Non-polymers285,475354
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 86505.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT6, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 96166.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT5, photosystem I

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Photosystem I reaction center subunit ... , 6 types, 18 molecules aDbDcDaEbEcEaFbFcFaIbIcIaLbLcLaMbMcM

#4: Protein Photosystem I reaction center subunit II


Mass: 15952.242 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NF26
#5: Protein Photosystem I reaction center subunit IV


Mass: 7468.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFW6
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 19931.127 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NH05
#7: Protein/peptide Photosystem I reaction center subunit Z / PSI-Z


Mass: 3853.611 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: P0C029
#9: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15806.324 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NIE7
#10: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3212.907 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NHY3

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Protein / Protein/peptide , 2 types, 6 molecules aCbCcCaJbJcJ

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8807.170 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NG86, photosystem I
#8: Protein/peptide Unknown protein


Mass: 2826.475 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421

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Non-polymers , 8 types, 756 molecules

#11: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 264 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical
ChemComp-1L3 / Menaquinone-4 / vitamin K2


Mass: 444.648 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H40O2
#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: PSI trimer / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.03 %DDM1
SpecimenConc.: 1.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 70.22 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.13_2998model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261743 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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