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- PDB-8t5u: ATP-1 state of Bcs1 (C7 symmetrized) -

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Basic information

Entry
Database: PDB / ID: 8t5u
TitleATP-1 state of Bcs1 (C7 symmetrized)
ComponentsMitochondrial chaperone BCS1
KeywordsTRANSLOCASE / Heptamer / AAA-ATPase / ATP-bound
Function / homology
Function and homology information


mitochondrial protein-transporting ATPase activity / mitochondrial respiratory chain complex IV assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex I assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding
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
ADENOSINE-5'-TRIPHOSPHATE / Mitochondrial chaperone BCS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsZhan, J. / Xia, D.
Funding support United States, 1items
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 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)344,33521
Polymers340,6157
Non-polymers3,72014
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "E"
d_7ens_1chain "G"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TYRTYRLEULEUFF47 - 41747 - 417
d_12ATPATPATPATPFS702
d_21TYRTYRLEULEUBB47 - 41747 - 417
d_22ATPATPATPATPBK702
d_31TYRTYRLEULEUCC47 - 41747 - 417
d_32ATPATPATPATPCM702
d_41TYRTYRLEULEUDD47 - 41747 - 417
d_42ATPATPATPATPDO702
d_51TYRTYRLEULEUAA47 - 41747 - 417
d_52ATPATPATPATPAI702
d_61TYRTYRLEULEUEE47 - 41747 - 417
d_62ATPATPATPATPEQ702
d_71TYRTYRLEULEUGG47 - 41747 - 417
d_72ATPATPATPATPGU702

NCS oper:
IDCodeMatrixVector
1given(-0.221993173122, -0.97504817299, 0.000302385454202), (0.97504811978, -0.22199328018, -0.00038427596236), (0.00044181511388, 0.00020953372833, 0.999999880448)350.086198266, 39.3850431398, -0.113114487927
2given(0.623655160643, -0.781699508369, 0.00034528063201), (0.78169955003, 0.623654940791, -0.000572983756287), (0.00023256514848, 0.00062724999125, 0.999999776235)184.491067418, -64.5205096518, -0.167796656996
3given(-0.8997051805, -0.436496804942, 0.00106181773322), (0.436497970075, -0.899704108959, 0.00142774072846), (0.000332117511288, 0.00174802701494, 0.999998417049)372.286025385, 232.97794819, -0.384168520806
4given(0.623644448204, 0.781707398385, 0.00107029650178), (-0.781708098034, 0.623644235493, 0.000563031803829), (-0.000227358117026, -0.00118779110136, 0.99999926873)-64.7477194636, 184.46263317, 0.28288385861
5given(-0.222193742029, 0.975000620229, 0.00193172353778), (-0.975002523605, -0.222193016466, -0.000585146967236), (-0.000141303176141, -0.00201345131853, 0.999997963022)39.1112659503, 350.220341759, 0.441663971417
6given(-0.90096887165, 0.433882589134, 0.00099557250337), (-0.433883690074, -0.900967414862, -0.00163120966922), (0.000189224909967, -0.0019016318066, 0.999998173994)233.652236665, 372.322330257, 0.366504017755

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Components

#1: Protein
Mitochondrial chaperone BCS1 / BCS1-like protein


Mass: 48659.281 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcs1l / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9CZP5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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 in uniform ATP-bound state captured during active ATPase cycle
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.34 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
9PHENIXmodel refinement
13cisTEM3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200466 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 145.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002623226
ELECTRON MICROSCOPYf_angle_d0.596631556
ELECTRON MICROSCOPYf_chiral_restr0.03793423
ELECTRON MICROSCOPYf_plane_restr0.00514032
ELECTRON MICROSCOPYf_dihedral_angle_d4.15033164
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2KBELECTRON MICROSCOPYNCS constraints2.83419893094E-12
ens_1d_3KBELECTRON MICROSCOPYNCS constraints5.00313304574E-11
ens_1d_4KBELECTRON MICROSCOPYNCS constraints8.73108501418E-13
ens_1d_5KBELECTRON MICROSCOPYNCS constraints5.01710686569E-13
ens_1d_6KBELECTRON MICROSCOPYNCS constraints1.98486441228E-11
ens_1d_7KBELECTRON MICROSCOPYNCS constraints9.18525245412E-11

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