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- EMDB-51537: Structure of the Rieske bound Apo1 state of the heptameric Bcs1 A... -

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Basic information

Entry
Database: EMDB / ID: EMD-51537
TitleStructure of the Rieske bound Apo1 state of the heptameric Bcs1 AAA-ATPase
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
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
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 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
BCS1, N-terminal / : / BCS1 N terminal / 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 ...BCS1, N-terminal / : / BCS1 N terminal / 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: 3.46 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 13, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51537.png

Downloads & links

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Map

FileDownload / File: emd_51537.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.274012 - 0.61713773
Average (Standard dev.)0.0039051205 (±0.033400033)
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: #2

Fileemd_51537_half_map_1.map
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Half map: #1

Fileemd_51537_half_map_2.map
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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
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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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: #1-#2
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 / 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

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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 / Number of copies: 1 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.587617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKVEVNLAAI PLGKNVVVKW QGKPVFIRHR TPHEIQEANS VDMSALKDPQ TDADRVKDPQ WLIMLGICTH LGCVPIGEAG DFGGWFCPC HGSHYDISGR IRKGPAPLNL EIPAYEFDGD KVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #3: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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