[English] 日本語
Yorodumi
- EMDB-41609: Bcs1 bound with ISP-ED -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41609
TitleBcs1 bound with ISP-ED
Map data
Sample
  • Complex: Bcs1 bound with ISP-ED
    • Complex: A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE BOVINE HEART MITOCHONDRIAL CYTOCHROME BC1-COMPLEX
      • Protein or peptide: RIESKE IRON-SULFUR PROTEIN
    • Complex: Mitochondrial chaperone BCS1
      • Protein or peptide: Mitochondrial chaperone BCS1
KeywordsHeptamer / TRANSLOCASE / AAA-ATPase / substrate-bound
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 / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial respiratory chain complex I assembly ...mitochondrial protein-transporting ATPase activity / protein insertion into mitochondrial inner membrane from matrix / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial respiratory chain complex I assembly / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
BCS1, N-terminal / BCS1 N terminal / BCS1_N / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / 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 ...BCS1, N-terminal / BCS1 N terminal / BCS1_N / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / 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] iron-sulphur domain / Rieske [2Fe-2S] 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 speciesBos taurus (cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 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
DepositionAug 14, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41609.png

Downloads & links

-
Map

FileDownload / File: emd_41609.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.03147263 - 0.15062071
Average (Standard dev.)0.0023294943 (±0.013218893)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_41609_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41609_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bcs1 bound with ISP-ED

EntireName: Bcs1 bound with ISP-ED
Components
  • Complex: Bcs1 bound with ISP-ED
    • Complex: A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE BOVINE HEART MITOCHONDRIAL CYTOCHROME BC1-COMPLEX
      • Protein or peptide: RIESKE IRON-SULFUR PROTEIN
    • Complex: Mitochondrial chaperone BCS1
      • Protein or peptide: Mitochondrial chaperone BCS1

-
Supramolecule #1: Bcs1 bound with ISP-ED

SupramoleculeName: Bcs1 bound with ISP-ED / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 340 KDa

-
Supramolecule #2: A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE...

SupramoleculeName: A WATER SOLUBLE FRAGMENT OF THE RIESKE IRON-SULFUR PROTEIN OF THE BOVINE HEART MITOCHONDRIAL CYTOCHROME BC1-COMPLEX
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle)

-
Supramolecule #3: Mitochondrial chaperone BCS1

SupramoleculeName: Mitochondrial chaperone BCS1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Mitochondrial chaperone BCS1

MacromoleculeName: Mitochondrial chaperone BCS1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MPFSDFVLAL KDNPYFGAGF GLVGVGTALA MARKGAQLGL VAFRRHYMIT LEVPARDRSY AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFIPS PGNHFIWYQG KWIRVERNRD MQMVDLQTGT PWESVTFTAL GTDRKVFFNI LEEARALALQ QEEGKTVMYT ...String:
MPFSDFVLAL KDNPYFGAGF GLVGVGTALA MARKGAQLGL VAFRRHYMIT LEVPARDRSY AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFIPS PGNHFIWYQG KWIRVERNRD MQMVDLQTGT PWESVTFTAL GTDRKVFFNI LEEARALALQ QEEGKTVMYT AVGSEWRTFG YPRRRRPLDS VVLQQGLADR IVKDIREFID NPKWYIDRGI PYRRGYLLYG PPGCGKSSFI TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPIK YQGLGRLTFS GLLNALDGVA STEARIVFMT TNYIDRLDPA LIRPGRVDLK EYVGYCSHWQ LTQMFQRFYP GQAPSLAENF AEHVLKATSE ISPAQVQGYF MLYKNDPMGA VHNIESLRHH HHHH

UniProtKB: Mitochondrial chaperone BCS1

-
Macromolecule #2: RIESKE IRON-SULFUR PROTEIN

MacromoleculeName: RIESKE IRON-SULFUR PROTEIN / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString:
VLAMSKIEIK LSDIPEGKNM AFKWRGKPLF VRHRTKKEID QEAAVEVSQL RDPQHDLERV KKPEWVILIG VCTHLGCVPI ANAGDFGGYY CPCHGSHYDA SGRIRKGPAP LNLEVPSYEF TSDDMVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: UltrAuFoil / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K

-
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

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8300
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more