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- EMDB-51562: Heptameric AAA-ATPase Bcs1 in the ATPgS2 state bound to Rieske-ISP -

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Basic information

Entry
Database: EMDB / ID: EMD-51562
TitleHeptameric AAA-ATPase Bcs1 in the ATPgS2 state bound to Rieske-ISP
Map data
Sample
  • Complex: Heptameric Bcs1 in complex with globular domain of the Rieske subunit of complex b-c1
    • Protein or peptide: Mitochondrial chaperone BCS1
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
KeywordsHeptameric complex Iron-sulfur cluster substrate / TRANSLOCASE
Function / homology
Function and homology information


protein insertion into mitochondrial inner membrane from matrix / Complex III assembly / : / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...protein insertion into mitochondrial inner membrane from matrix / Complex III assembly / : / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
BCS1, N-terminal / : / BCS1 N terminal / Mitochondrial chaperone BCS1-like, ATPase lid domain / BCS1_N / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal ...BCS1, N-terminal / : / BCS1 N terminal / Mitochondrial chaperone BCS1-like, ATPase lid domain / BCS1_N / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / 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
Cytochrome b-c1 complex subunit Rieske, mitochondrial / Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 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 17, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51562.png

Downloads & links

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Map

FileDownload / File: emd_51562.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.29767895 - 0.82770944
Average (Standard dev.)0.0029954817 (±0.03435825)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_51562_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_51562_half_map_2.map
Projections & Slices
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Sample components

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Entire : Heptameric Bcs1 in complex with globular domain of the Rieske sub...

EntireName: Heptameric Bcs1 in complex with globular domain of the Rieske subunit of complex b-c1
Components
  • Complex: Heptameric Bcs1 in complex with globular domain of the Rieske subunit of complex b-c1
    • Protein or peptide: Mitochondrial chaperone BCS1
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Supramolecule #1: Heptameric Bcs1 in complex with globular domain of the Rieske sub...

SupramoleculeName: Heptameric Bcs1 in complex with globular domain of the Rieske subunit of complex b-c1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Mitochondrial chaperone BCS1

MacromoleculeName: Mitochondrial chaperone BCS1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGKHHHHHHG GGDYKDDDDK GSGHMSDKPI DIQYDKQATP NLSGVITPPT NETGNDSVR EKLSKLVGDA MSNNPYFAAG GGLMILGTGL AVARSGIIKA S RVLYRQMI VDLEIQSKDK SYAWFLTWMA KHPQRVSRHL SVRTNYIQHD NG SVSTKFS LVPGPGNHWI ...String:
MGKHHHHHHG GGDYKDDDDK GSGHMSDKPI DIQYDKQATP NLSGVITPPT NETGNDSVR EKLSKLVGDA MSNNPYFAAG GGLMILGTGL AVARSGIIKA S RVLYRQMI VDLEIQSKDK SYAWFLTWMA KHPQRVSRHL SVRTNYIQHD NG SVSTKFS LVPGPGNHWI RYKGAFILIK RERSAKMIDI ANGSPFETVT LTT LYRDKH LFDDILNEAK DIALKTTEGK TVIYTSFGPE WRKFGQPKAK RMLP SVILD SGIKEGILDD VYDFMKNGKW YSDRGIPYRR GYLLYGPPGS GKTSF IQAL AGELDYNICI LNLSENNLTD DRLNHLMNNM PERSILLLED IDAAFN KRS QTGEQGFHSS VTFSGLLNAL DGVTSSEETI TFMTTNHPEK LDAAIMR PG RIDYKVFVGN ATPYQVEKMF MKFYPGETDI CKKFVNSVKE LDITVSTA Q LQGLFVMNKD APHDALKMVS SLRNANHIF

UniProtKB: Mitochondrial chaperone BCS1

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Macromolecule #2: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTATADVLAM AKVEVNLAAI PLGKNVVVKW QGKPVFIRHR TPHEIQEANS VDMSALKDPQ TDADRVKDPQ WLIMLGICTH LGCVPIGEAG DFGGWFCPCH GSHYDISGRI RKGPAPLNLE IPAYEFDGDK VIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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