[English] 日本語
Yorodumi
- PDB-7vzr: Structure of the Acidobacteria homodimeric reaction center bound ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more