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- EMDB-41095: ADP-bound Bcs1 (unsymmetrized) -

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Basic information

Entry
Database: EMDB / ID: EMD-41095
TitleADP-bound Bcs1 (unsymmetrized)
Map data
Sample
  • Complex: Heptameric Bcs1 in uniform ADP-bound state captured in active ATPase cycle in the presence of substrate ISP-ED, unsymmetrized
    • Protein or peptide: Mitochondrial chaperone BCS1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHeptamer / ADP-bound / TRANSLOCASE / AAA-ATPase
Function / homology
Function and homology information


mitochondrial protein-transporting ATPase activity / protein insertion into mitochondrial inner membrane from matrix / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex I assembly / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding
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
Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsZhan J / Xia D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2024
Title: Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate.
Authors: Jingyu Zhan / Allison Zeher / Rick Huang / Wai Kwan Tang / Lisa M Jenkins / Di Xia /
Abstract: The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how ...The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.
History
DepositionJun 21, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41095.png

Downloads & links

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Map

FileDownload / File: emd_41095.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.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.14015576 - 0.3448614
Average (Standard dev.)0.0023265514 (±0.014565632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41095_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_41095_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_41095_half_map_2.map
Projections & Slices
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Sample components

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Entire : Heptameric Bcs1 in uniform ADP-bound state captured in active ATP...

EntireName: Heptameric Bcs1 in uniform ADP-bound state captured in active ATPase cycle in the presence of substrate ISP-ED, unsymmetrized
Components
  • Complex: Heptameric Bcs1 in uniform ADP-bound state captured in active ATPase cycle in the presence of substrate ISP-ED, unsymmetrized
    • Protein or peptide: Mitochondrial chaperone BCS1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Heptameric Bcs1 in uniform ADP-bound state captured in active ATP...

SupramoleculeName: Heptameric Bcs1 in uniform ADP-bound state captured in active ATPase cycle in the presence of substrate ISP-ED, unsymmetrized
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 340 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: Mus musculus (house mouse)
Molecular weightTheoretical: 48.289887 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MPFSDFVLAL KDNPYFGAGF GLVGVGTALA MARKGAQLGL VAFRRHYMIT LEVPARDRSY AWLLSWLTRH STRTQHLSVE TSYLQHESG RISTKFEFIP SPGNHFIWYQ GKWIRVERNR DMQMVDLQTG TPWESVTFTA LGTDRKVFFN ILEEARALAL Q QEEGKTVM ...String:
MPFSDFVLAL KDNPYFGAGF GLVGVGTALA MARKGAQLGL VAFRRHYMIT LEVPARDRSY AWLLSWLTRH STRTQHLSVE TSYLQHESG RISTKFEFIP SPGNHFIWYQ GKWIRVERNR DMQMVDLQTG TPWESVTFTA LGTDRKVFFN ILEEARALAL Q QEEGKTVM YTAVGSEWRT FGYPRRRRPL DSVVLQQGLA DRIVKDIREF IDNPKWYIDR GIPYRRGYLL YGPPGCGKSS FI TALAGEL EHSICLLSLT DSSLSDDRLN HLLSVAPQQS LVLLEDVDAA FLSRDLAVEN PIKYQGLGRL TFSGLLNALD GVA STEARI VFMTTNYIDR LDPALIRPGR VDLKEYVGYC SHWQLTQMFQ RFYPGQAPSL AENFAEHVLK ATSEISPAQV QGYF MLYKN DPMGAVHNIE SLRHHHHHH

UniProtKB: Mitochondrial chaperone BCS1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 7 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 8
GridModel: UltrAuFoil / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 37681
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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