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- PDB-7vzr: Structure of the Acidobacteria homodimeric reaction center bound ... -

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Basic information

Entry
Database: PDB / ID: 7vzr
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the smaller form)
Components
  • Cytochrome c domain-containing protein
  • Cytochrome c, mono-and diheme variants
  • Photosynthetic reaction center subunit M
  • PscE
  • PscF
  • PscG
  • undefined polypeptide
KeywordsPHOTOSYNTHESIS / membrane protein
Function / homology
Function and homology information


thylakoid / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane
Similarity search - Function
Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain ...Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2GO / Chem-84Q / Chem-85I / Chem-85N / BACTERIOCHLOROPHYLL A / CHLOROPHYLL A / HEME C / LYCOPENE / IRON/SULFUR CLUSTER / Unknown ligand ...Chem-2GO / Chem-84Q / Chem-85I / Chem-85N / BACTERIOCHLOROPHYLL A / CHLOROPHYLL A / HEME C / LYCOPENE / IRON/SULFUR CLUSTER / Unknown ligand / Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria)
Chloracidobacterium thermophilum B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsHuang, G.Q. / Dong, S.S. / Qin, X.C. / Sui, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c
Authors: Dong, S. / Huang, G. / Wang, C. / Wang, J. / Sui, S.F. / Qin, X.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosynthetic reaction center subunit M
C: Cytochrome c, mono-and diheme variants
E: PscE
F: PscF
G: PscG
H: undefined polypeptide
a: Photosynthetic reaction center subunit M
c: Cytochrome c domain-containing protein
e: PscE
f: PscF
g: PscG
h: undefined polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,51791
Polymers266,91812
Non-polymers57,59979
Water1086
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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Protein , 3 types, 4 molecules AaCc

#1: Protein Photosynthetic reaction center subunit M


Mass: 99311.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LDR8
#2: Protein Cytochrome c, mono-and diheme variants


Mass: 24138.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LDR4
#7: Protein Cytochrome c domain-containing protein


Mass: 15664.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LDR3

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Protein/peptide , 4 types, 8 molecules EeFfGgHh

#3: Protein/peptide PscE


Mass: 3684.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LK98
#4: Protein/peptide PscF


Mass: 3885.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LEN5
#5: Protein/peptide PscG


Mass: 5041.152 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum B (bacteria)
References: UniProt: G2LJ20
#6: Protein/peptide undefined polypeptide


Mass: 1635.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloracidobacterium thermophilum (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 12 types, 85 molecules

#8: Chemical ChemComp-2GO / [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc


Mass: 948.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H70N4O6Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-LYC / LYCOPENE


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#13: Chemical
ChemComp-85I / [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate


Mass: 663.906 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H70NO8P / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 671.023 Da / Num. of mol.: 32 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-85N / [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium


Mass: 671.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76NO7 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-84Q / [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate / 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine


Mass: 649.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H68NO8P / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: CabRC complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490075 / Symmetry type: POINT
RefinementHighest resolution: 2.22 Å

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