+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10192 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the ADP state of the heptameric Bcs1 AAA-ATPase | |||||||||
Map data | C7 symmetrized map of the Bcs1 ADP state resolved at 3.4 A after relion postprocessing. | |||||||||
Sample |
| |||||||||
Keywords | translocation / Rieske / mitochondira / inner mitochondiral membrane / TRANSLOCASE | |||||||||
Function / homology | Function and homology information protein insertion into mitochondrial inner membrane from matrix / mitochondrial respiratory chain complex III assembly / chaperone-mediated protein complex assembly / protein transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Kater L / Beckmann R | |||||||||
Citation | 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10192.map.gz | 60 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10192-v30.xml emd-10192.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10192_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_10192.png | 134.8 KB | ||
Filedesc metadata | emd-10192.cif.gz | 5.3 KB | ||
Others | emd_10192_additional_1.map.gz emd_10192_additional_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10192 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10192 | HTTPS FTP |
-Validation report
Summary document | emd_10192_validation.pdf.gz | 316.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10192_full_validation.pdf.gz | 315.7 KB | Display | |
Data in XML | emd_10192_validation.xml.gz | 10.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10192 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10192 | HTTPS FTP |
-Related structure data
Related structure data | 6sh3MC 6sh4C 6sh5C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_10192.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | C7 symmetrized map of the Bcs1 ADP state resolved at 3.4 A after relion postprocessing. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: C7 symmetrized map of the Bcs1 ADP state...
File | emd_10192_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | C7 symmetrized map of the Bcs1 ADP state resolved at 3.4 A after relion local resolution filtering. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: C7 symmetrized map of the Bcs1 ADP state...
File | emd_10192_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | C7 symmetrized map of the Bcs1 ADP state resolved at 3.4 A after relion local resolution filtering. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Heptameric complex of ADP bound Bcs1
Entire | Name: Heptameric complex of ADP bound Bcs1 |
---|---|
Components |
|
-Supramolecule #1: Heptameric complex of ADP bound Bcs1
Supramolecule | Name: Heptameric complex of ADP bound Bcs1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Mitochondrial chaperone BCS1
Macromolecule | Name: Mitochondrial chaperone BCS1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 51.172336 KDa |
Sequence | String: MSDKPIDIQY DKQATPNLSG VITPPTNETG NDSVREKLSK LVGDAMSNNP YFAAGGGLMI LGTGLAVARS GIIKASRVLY RQMIVDLEI QSKDKSYAWF LTWMAKHPQR VSRHLSVRTN YIQHDNGSVS TKFSLVPGPG NHWIRYKGAF ILIKRERSAK M IDIANGSP ...String: MSDKPIDIQY DKQATPNLSG VITPPTNETG NDSVREKLSK LVGDAMSNNP YFAAGGGLMI LGTGLAVARS GIIKASRVLY RQMIVDLEI QSKDKSYAWF LTWMAKHPQR VSRHLSVRTN YIQHDNGSVS TKFSLVPGPG NHWIRYKGAF ILIKRERSAK M IDIANGSP FETVTLTTLY RDKHLFDDIL NEAKDIALKT TEGKTVIYTS FGPEWRKFGQ PKAKRMLPSV ILDSGIKEGI LD DVYDFMK NGKWYSDRGI PYRRGYLLYG PPGSGKTSFI QALAGELDYN ICILNLSENN LTDDRLNHLM NNMPERSILL LED IDAAFN KRSQTGEQGF HSSVTFSGLL NALDGVTSSE ETITFMTTNH PEKLDAAIMR PGRIDYKVFV GNATPYQVEK MFMK FYPGE TDICKKFVNS VKELDITVST AQLQGLFVMN KDAPHDALKM VSSLRNANHI F UniProtKB: Mitochondrial chaperone BCS1 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 7 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 12.0 sec. / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |