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

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Basic information

Entry
Database: PDB / ID: 7vzg
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form)
Components
  • Cytochrome c domain-containing protein
  • Cytochrome c, mono-and diheme variants
  • Photosystem P840 reaction center iron-sulfur protein
  • PscA
  • PscD'
  • PscE
  • PscF
  • PscG
  • undefined polypeptide
KeywordsPHOTOSYNTHESIS / membrane protein
Function / homology
Function and homology information


thylakoid / iron-sulfur cluster binding / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding
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 / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...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 / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
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 / Photosystem P840 reaction center iron-sulfur protein / Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Uncharacterized protein / Uncharacterized protein / UPF0291 protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 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: Shishang Dong / Guoqiang Huang / Changhui Wang / Jiajia Wang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer ...Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 FeS clusters, 12 lipids, 2 Ca ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PscA
C: Cytochrome c, mono-and diheme variants
E: PscE
F: PscF
G: PscG
H: undefined polypeptide
a: PscA
c: Cytochrome c domain-containing protein
e: PscE
f: PscF
g: PscG
h: undefined polypeptide
B: Photosystem P840 reaction center iron-sulfur protein
D: PscD'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,00395
Polymers278,92914
Non-polymers58,07481
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 , 5 types, 6 molecules AaCcBD

#1: Protein PscA


Mass: 98537.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (bacteria)
References: UniProt: G2LDR8
#2: Protein Cytochrome c, mono-and diheme variants


Mass: 22369.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (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 (bacteria)
References: UniProt: G2LDR3
#8: Protein Photosystem P840 reaction center iron-sulfur protein


Mass: 8199.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (bacteria)
References: UniProt: A8DJF8
#9: Protein PscD'


Mass: 8622.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (bacteria)
References: UniProt: G2LHG2

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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 (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 (bacteria)
References: UniProt: G2LEN5
#5: Protein/peptide PscG


Mass: 4293.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (bacteria)
References: UniProt: G2LJ20
#6: Protein/peptide undefined polypeptide


Mass: 1635.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloracidobacterium thermophilum (bacteria)

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Non-polymers , 12 types, 87 molecules

#10: 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
#11: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#15: 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
#16: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 663.906 Da / Num. of mol.: 32 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#17: 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
#18: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#19: 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
#20: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#21: 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, the larger form / Type: COMPLEX / Entity ID: #1-#9 / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52612 / Symmetry type: POINT

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