[English] 日本語
Yorodumi
- EMDB-51552: Structure of the ATPgS-S1 state of the heptameric Bcs1 AAA-ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51552
TitleStructure of the ATPgS-S1 state of the heptameric Bcs1 AAA-ATPase
Map data
Sample
  • Complex: Heptameric Bcs1 bound to ATPgS in conformational state S1
    • Protein or peptide: Mitochondrial chaperone BCS1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsHeptameric complex / TRANSLOCASE / mitochondrial
Function / homology
Function and homology information


protein insertion into mitochondrial inner membrane from matrix / mitochondrial respiratory chain complex III assembly / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion ...protein insertion into mitochondrial inner membrane from matrix / mitochondrial respiratory chain complex III assembly / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
BCS1, N-terminal / : / BCS1 N terminal / Mitochondrial chaperone BCS1-like, ATPase lid domain / BCS1_N / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities ...BCS1, N-terminal / : / BCS1 N terminal / Mitochondrial chaperone BCS1-like, ATPase lid domain / BCS1_N / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsRosales-Hernandez C / Beckmann R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure of the Bcs1 AAA-ATPase suggests an airlock-like translocation mechanism for folded proteins.
Authors: Lukas Kater / Nikola Wagener / Otto Berninghausen / Thomas Becker / Walter Neupert / Roland Beckmann /
Abstract: Some proteins require completion of folding before translocation across a membrane into another cellular compartment. Yet the permeability barrier of the membrane should not be compromised and ...Some proteins require completion of folding before translocation across a membrane into another cellular compartment. Yet the permeability barrier of the membrane should not be compromised and mechanisms have remained mostly elusive. Here, we present the structure of Saccharomyces cerevisiae Bcs1, an AAA-ATPase of the inner mitochondrial membrane. Bcs1 facilitates the translocation of the Rieske protein, Rip1, which requires folding and incorporation of a 2Fe-2S cluster before translocation and subsequent integration into the bc1 complex. Surprisingly, Bcs1 assembles into exclusively heptameric homo-oligomers, with each protomer consisting of an amphipathic transmembrane helix, a middle domain and an ATPase domain. Together they form two aqueous vestibules, the first being accessible from the mitochondrial matrix and the second positioned in the inner membrane, with both separated by the seal-forming middle domain. On the basis of this unique architecture, we propose an airlock-like translocation mechanism for folded Rip1.
History
DepositionSep 16, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51552.png

Downloads & links

-
Map

FileDownload / File: emd_51552.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.27416977 - 0.88254225
Average (Standard dev.)0.00108114 (±0.033919092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_51552_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51552_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heptameric Bcs1 bound to ATPgS in conformational state S1

EntireName: Heptameric Bcs1 bound to ATPgS in conformational state S1
Components
  • Complex: Heptameric Bcs1 bound to ATPgS in conformational state S1
    • Protein or peptide: Mitochondrial chaperone BCS1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Heptameric Bcs1 bound to ATPgS in conformational state S1

SupramoleculeName: Heptameric Bcs1 bound to ATPgS in conformational state S1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Mitochondrial chaperone BCS1

MacromoleculeName: Mitochondrial chaperone BCS1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 53.826086 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGKHHHHHHG GGDYKDDDDK GSGHMSDKPI DIQYDKQATP NLSGVITPPT NETGNDSVRE KLSKLVGDAM SNNPYFAAGG GLMILGTGL AVARSGIIKA SRVLYRQMIV DLEIQSKDKS YAWFLTWMAK HPQRVSRHLS VRTNYIQHDN GSVSTKFSLV P GPGNHWIR ...String:
MGKHHHHHHG GGDYKDDDDK GSGHMSDKPI DIQYDKQATP NLSGVITPPT NETGNDSVRE KLSKLVGDAM SNNPYFAAGG GLMILGTGL AVARSGIIKA SRVLYRQMIV DLEIQSKDKS YAWFLTWMAK HPQRVSRHLS VRTNYIQHDN GSVSTKFSLV P GPGNHWIR YKGAFILIKR ERSAKMIDIA NGSPFETVTL TTLYRDKHLF DDILNEAKDI ALKTTEGKTV IYTSFGPEWR KF GQPKAKR MLPSVILDSG IKEGILDDVY DFMKNGKWYS DRGIPYRRGY LLYGPPGSGK TSFIQALAGE LDYNICILNL SEN NLTDDR LNHLMNNMPE RSILLLEDID AAFNKRSQTG EQGFHSSVTF SGLLNALDGV TSSEETITFM TTNHPEKLDA AIMR PGRID YKVFVGNATP YQVEKMFMKF YPGETDICKK FVNSVKELDI TVSTAQLQGL FVMNKDAPHD ALKMVSSLRN ANHIF

UniProtKB: Mitochondrial chaperone BCS1

-
Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 7 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141861
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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