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- PDB-9gu9: Structure of the ATPgS-S2 state of the heptameric Bcs1 AAA-ATPase -

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Basic information

Entry
Database: PDB / ID: 9gu9
TitleStructure of the ATPgS-S2 state of the heptameric Bcs1 AAA-ATPase
ComponentsMitochondrial chaperone BCS1
KeywordsTRANSLOCASE / Heptameric complex / mitochondrial
Function / homology
Function and homology information


protein insertion into mitochondrial inner membrane from matrix / mitochondrial respiratory chain complex III assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion ...protein insertion into mitochondrial inner membrane from matrix / mitochondrial respiratory chain complex III assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / chaperone-mediated protein complex assembly / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
BCS1, N-terminal / : / BCS1 N terminal / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsRosales-Hernandez, C. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: EMBO J / Year: 2025
Title: Mechanistic insights into Bcs1-mediated mitochondrial membrane translocation of the folded Rieske protein.
Authors: Cristian Rosales-Hernandez / Matthias Thoms / Otto Berninghausen / Thomas Becker / Roland Beckmann /
Abstract: A functional mitochondrial respiratory chain requires coordinated and tightly regulated assembly of mitochondrial- and nuclear-encoded subunits. For bc1 complex (complex III) assembly, the iron- ...A functional mitochondrial respiratory chain requires coordinated and tightly regulated assembly of mitochondrial- and nuclear-encoded subunits. For bc1 complex (complex III) assembly, the iron-sulfur protein Rip1 must first be imported into the mitochondrial matrix to fold and acquire its 2Fe-2S cluster, then translocated and inserted into the inner mitochondrial membrane (IM). This translocation of folded Rip1 is accomplished by Bcs1, an unusual heptameric AAA ATPase that couples ATP hydrolysis to translocation. However, the molecular and mechanistic details of Bcs1-mediated Rip1 translocation have remained elusive. Here, we provide structural and biochemical evidence on how Bcs1 alternates between conformational states to translocate Rip1 across the IM. Using cryo-electron microscopy (cryo-EM), we identified substrate-bound pre-translocation and pre-release states, revealing how electrostatic interactions promote Rip1 binding to Bcs1. An ATP-induced conformational switch of the Bcs1 heptamer facilitates Rip1 translocation between two distinct aqueous vestibules-one exposed to the matrix, the other to the intermembrane space-in an airlock-like mechanism. This would minimize disruption of the IM permeability barrier, which could otherwise lead to proton leakage and compromised mitochondrial energy conversion.
#1: Journal: 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 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial chaperone BCS1
B: Mitochondrial chaperone BCS1
C: Mitochondrial chaperone BCS1
D: Mitochondrial chaperone BCS1
E: Mitochondrial chaperone BCS1
F: Mitochondrial chaperone BCS1
G: Mitochondrial chaperone BCS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,44514
Polymers376,7837
Non-polymers3,6637
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Mitochondrial chaperone BCS1


Mass: 53826.086 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BCS1, YDR375C, D9481.17 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32839
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Heptameric Bcs1 bound to ATPgS in conformational state S2
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92248 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422043
ELECTRON MICROSCOPYf_angle_d0.77529820
ELECTRON MICROSCOPYf_dihedral_angle_d8.1662989
ELECTRON MICROSCOPYf_chiral_restr0.043304
ELECTRON MICROSCOPYf_plane_restr0.0043752

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