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Basic information

Entry
Database: PDB / ID: 7fix
TitleCryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
Components
  • (Photosystem I ...) x 12
  • Ferredoxin-1
KeywordsPHOTOSYNTHESIS / Photosystem I / Ferredoxin / Cytochrome c6
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Electron transport accessory-like domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / [2Ga-2S] cluster / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Ferredoxin-1 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / [2Ga-2S] cluster / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Ferredoxin-1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.97 Å
AuthorsLi, J. / Kurisu, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 Å resolution.
Authors: Jiannan Li / Noriyuki Hamaoka / Fumiaki Makino / Akihiro Kawamoto / Yuxi Lin / Matthias Rögner / Marc M Nowaczyk / Young-Ho Lee / Keiichi Namba / Christoph Gerle / Genji Kurisu /
Abstract: Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of ...Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of structural detail concerning PSI:Fd interface and the possible binding sites of Cyt c. Here we describe the high resolution cryo-EM structure of Thermosynechococcus elongatus BP-1 PSI in complex with Fd and a loosely bound Cyt c. Side chain interactions at the PSI:Fd interface including bridging water molecules are visualized in detail. The structure explains the properties of mutants of PsaE and PsaC that affect kinetics of Fd binding and suggests a molecular switch for the dissociation of Fd upon reduction. Calorimetry-based thermodynamic analyses confirms a single binding site for Fd and demonstrates that PSI:Fd complexation is purely driven by entropy. A possible reaction cycle for the efficient transfer of electrons from Cyt c to Fd via PSI is proposed.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _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
A1: Photosystem I P700 chlorophyll a apoprotein A1
B1: Photosystem I P700 chlorophyll a apoprotein A2
C1: Photosystem I iron-sulfur center
D1: Photosystem I reaction center subunit II
E1: Photosystem I reaction center subunit IV
F1: Photosystem I reaction center subunit III
I1: Photosystem I reaction center subunit VIII
J1: Photosystem I reaction center subunit IX
K1: Photosystem I reaction center subunit PsaK
L1: Photosystem I reaction center subunit XI
M1: Photosystem I reaction center subunit XII
R1: Ferredoxin-1
X1: Photosystem I 4.8K protein
A2: Photosystem I P700 chlorophyll a apoprotein A1
B2: Photosystem I P700 chlorophyll a apoprotein A2
C2: Photosystem I iron-sulfur center
D2: Photosystem I reaction center subunit II
E2: Photosystem I reaction center subunit IV
F2: Photosystem I reaction center subunit III
I2: Photosystem I reaction center subunit VIII
J2: Photosystem I reaction center subunit IX
K2: Photosystem I reaction center subunit PsaK
L2: Photosystem I reaction center subunit XI
M2: Photosystem I reaction center subunit XII
R2: Ferredoxin-1
X2: Photosystem I 4.8K protein
A3: Photosystem I P700 chlorophyll a apoprotein A1
B3: Photosystem I P700 chlorophyll a apoprotein A2
C3: Photosystem I iron-sulfur center
D3: Photosystem I reaction center subunit II
E3: Photosystem I reaction center subunit IV
F3: Photosystem I reaction center subunit III
I3: Photosystem I reaction center subunit VIII
J3: Photosystem I reaction center subunit IX
K3: Photosystem I reaction center subunit PsaK
L3: Photosystem I reaction center subunit XI
M3: Photosystem I reaction center subunit XII
R3: Ferredoxin-1
X3: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,125,795483
Polymers811,81739
Non-polymers313,978444
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 12 types, 36 molecules A1A2A3B1B2B3C1C2C3D1D2D3E1E2E3F1F2F3I1I2I3J1J2J3K1K2K3L1L2L3...

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


Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 19098.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / Gene: psaF, tlr2411
Production host: Thermosynechococcus vestitus BP-1 (bacteria)
Strain (production host): BP-1 / References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4297.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4770.698 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16261.685 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P0A403
#13: Protein/peptide Photosystem I 4.8K protein


Mass: 4424.317 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / Gene: tsr0813
Production host: Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DKP6

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Protein / Sugars , 2 types, 6 molecules R1R2R3

#12: Protein Ferredoxin-1 / Ferredoxin I


Mass: 10853.959 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / Gene: petF1, petF / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3C9
#21: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 10 types, 789 molecules

#14: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 285 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#20: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 40.078 Da / Num. of mol.: 51 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-GAK / [2Ga-2S] cluster


Mass: 203.576 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ga2S2 / Feature type: SUBJECT OF INVESTIGATION
#24: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6COMPLEXCytochrome C6 was not be built in model because of limited resolution#1-#130MULTIPLE SOURCES
2Photosystem I trimerCOMPLEX12 subunits with 10x his-tag on N-ter of PsaF in each monomer.#1-#5, #7-#111MULTIPLE SOURCES
3Ga-Substituted FerredoxinCOMPLEX#6, #12-#131RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.11 MDaYES
211.08 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Thermosynechococcus elongatus BP-1 (bacteria)197221
33Thermosynechococcus elongatus BP-1 (bacteria)197221
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 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 / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 1.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207142 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009977472
ELECTRON MICROSCOPYf_angle_d1.0595109821
ELECTRON MICROSCOPYf_chiral_restr0.04529600
ELECTRON MICROSCOPYf_plane_restr0.00524132
ELECTRON MICROSCOPYf_dihedral_angle_d10.624435637

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