[English] 日本語
Yorodumi
- EMDB-32229: Structure of the Acidobacteria homodimeric reaction center bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32229
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the smaller form)
Map data
Sample
  • Complex: CabRC complex
    • Protein or peptide: x 7 types
  • Ligand: x 12 types
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 family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Photosynthetic reaction center subunit M / Cytochrome b6-f complex subunit PetG / Stage III sporulation protein AF / MetS family NSS transporter small subunit
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria) / Chloracidobacterium thermophilum B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsHuang GQ / Dong SS / Qin XC / Sui SF
Funding support1 items
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 SF / Qin X
History
DepositionNov 16, 2021-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32229.png

Downloads & links

-
Map

FileDownload / File: emd_32229.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-2.8086092 - 5.660906
Average (Standard dev.)0.008958789 (±0.16378304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 238.15 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : CabRC complex

EntireName: CabRC complex
Components
  • Complex: CabRC complex
    • Protein or peptide: Photosynthetic reaction center subunit MPhotosynthetic reaction centre
    • Protein or peptide: Cytochrome c, mono-and diheme variants
    • Protein or peptide: PscE
    • Protein or peptide: PscF
    • Protein or peptide: PscG
    • Protein or peptide: undefined polypeptide
    • Protein or peptide: Cytochrome c domain-containing protein
  • Ligand: [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
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: CHLOROPHYLL A
  • Ligand: LYCOPENE
  • Ligand: CALCIUM IONCalcium
  • Ligand: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: UNKNOWN LIGAND
  • Ligand: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
  • Ligand: HEME C
  • Ligand: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: water

+
Supramolecule #1: CabRC complex

SupramoleculeName: CabRC complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)

+
Macromolecule #1: Photosynthetic reaction center subunit M

MacromoleculeName: Photosynthetic reaction center subunit M / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 99.311414 KDa
SequenceString: MASFSSYANG VKRWYQKLEL PMPPERIFGA HMMLIGGLAC LIGTYFFASM TMWNDGYVNL TLRPRLISLG IYDPYDTEQI QRVWLPLIG EFSTSKLPFF GQYPLTMTDF RLFGWGCFHI GLGLWLVYAG AAHYYGARGG ATIGEIFWLL PYVPGLKGLC Q IKWFTPEG ...String:
MASFSSYANG VKRWYQKLEL PMPPERIFGA HMMLIGGLAC LIGTYFFASM TMWNDGYVNL TLRPRLISLG IYDPYDTEQI QRVWLPLIG EFSTSKLPFF GQYPLTMTDF RLFGWGCFHI GLGLWLVYAG AAHYYGARGG ATIGEIFWLL PYVPGLKGLC Q IKWFTPEG PWYKVGLPWG SFANTPWPIL RRTYADALSP HTIYIGLLFF IWGFVLWFVL DKPPVPLQPA QVMTPNGLMP LE QAPFPYG WFDPYLNQVM HPMNTINGET TMCFVWGVLF VALGAYWWYR PPRSINITHL EDTKAVFHVH LTAIGYVSFA LAI VGFLAL RNHPSYLMLN DMNVIIYGKK IVNPGRMIHN MITFNHVQVG LLYVAAGVFH GGQYLHGLNI SGAYKQARSK FITW FQNPD LQTKIVGTTM FVSFVTVVFG YGMICWNTGA ELDLNFGIYQ FRSFRAIQMD GEAGNIGYRV FRPKNPWDPT AGGDW VKNP DGTAKLVKAR NLQVGDRILN EELGIGSSPT YSFTTIEEIN YKPEWGQPKL YAVQWGSWTH FLRKVNPLFW VDKGIW YLQ NQKTFEATRK ADEAYLAAHL KAVSLLNQID DAQTEEAKQK AQAELDKFRP ELEKAHANML EWNERLASTP AVLYSNL RD QHRDGEINDA IFFWLMIGGW LFGFIPLLRI AFHNYQSPWY RDFEWRKQSP DFPCIGPVKG GTCGVSIQDQ LWFCILFS I KPLSAIAWYL DGGWIATMMA RGNEAYYLTH NISHTGGVFL YMWNETTWIW TDNHLTAMLL LGHLIWFVSF ALWFKDRGS RAEGGDIQSR WVRLMGKRLG IKTLQEVRFP VSNLATAKLW GTVFFYTGTF VLVFLYFADG FFQNR

+
Macromolecule #2: Cytochrome c, mono-and diheme variants

MacromoleculeName: Cytochrome c, mono-and diheme variants / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 24.138053 KDa
SequenceString: MKSIKIIVLG SALALLVGGC FVGSRDPNET RYPKAPMPLQ NQTSTLKTAE EIRRESVAQN TPGAREAAAL RDRVTPLNLQ QVNEQDVAG NDPLGSPARV VLDEGEMYRD PVEIYREGRA LFQNNCVGCH GHNGCGNVPR STNFTDPGWQ ENNSDGGIYS S IYNGKGIG ...String:
MKSIKIIVLG SALALLVGGC FVGSRDPNET RYPKAPMPLQ NQTSTLKTAE EIRRESVAQN TPGAREAAAL RDRVTPLNLQ QVNEQDVAG NDPLGSPARV VLDEGEMYRD PVEIYREGRA LFQNNCVGCH GHNGCGNVPR STNFTDPGWQ ENNSDGGIYS S IYNGKGIG NGGGAMPAYY NQLSPQQIRY LVAYLRAFKG RQCNGLPTLS DVERMVAERQ NKP

+
Macromolecule #3: PscE

MacromoleculeName: PscE / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 3.684458 KDa
SequenceString:
MTAILLACLF VLGGYAALWG IIKFVVANTK DIAAN

+
Macromolecule #4: PscF

MacromoleculeName: PscF / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 3.885684 KDa
SequenceString:
MWNVVGQIIS VLCFFILTVG TLFGIVYVSH LLSRG

+
Macromolecule #5: PscG

MacromoleculeName: PscG / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 5.041152 KDa
SequenceString:
MEGVAMEDIS KVAWAWFGVL LAICLIGAFG NYVPKLFVKM LMFLN

+
Macromolecule #6: undefined polypeptide

MacromoleculeName: undefined polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 1.635006 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #7: Cytochrome c domain-containing protein

MacromoleculeName: Cytochrome c domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum B (bacteria)
Molecular weightTheoretical: 15.664669 KDa
SequenceString:
VMATGCFVGA RNASEPRLGS SSIAASRTAP AYLREAQVLY EGSTDGLPKD TPADEIAHYK AMLAELQTRN YAACAGCHQV NGGGNKAIN ATNFQDAGWQ ANNSSPGMVT SIVNGKGKVM PAYKDKLTLQ QINYLVEYIR RFEKKR

+
Macromolecule #8: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-o...

MacromoleculeName: [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
type: ligand / ID: 8 / Number of copies: 2 / Formula: 2GO
Molecular weightTheoretical: 948.576 Da
Chemical component information

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

+
Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 16 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

+
Macromolecule #10: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 10 / Number of copies: 10 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #11: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 11 / Number of copies: 2 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE / Lycopene

+
Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #13: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-m...

MacromoleculeName: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 13 / Number of copies: 6 / Formula: 85I
Molecular weightTheoretical: 663.906 Da
Chemical component information

ChemComp-85I:
[(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

+
Macromolecule #14: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 14 / Number of copies: 32 / Formula: UNL
Molecular weightTheoretical: 671.023 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

+
Macromolecule #15: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]met...

MacromoleculeName: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
type: ligand / ID: 15 / Number of copies: 4 / Formula: 85N
Molecular weightTheoretical: 671.023 Da
Chemical component information

ChemComp-85N:
[(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium

+
Macromolecule #16: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 16 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #17: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetra...

MacromoleculeName: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 17 / Number of copies: 2 / Formula: 84Q
Molecular weightTheoretical: 649.879 Da
Chemical component information

ChemComp-84Q:
[(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

+
Macromolecule #18: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 18 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

+
Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 490075

+
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://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