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Yorodumi- PDB-8qxv: In situ structure average of GroEL14-GroES7 complexes with narrow... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qxv | ||||||
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Title | In situ structure average of GroEL14-GroES7 complexes with narrow GroEL7 trans ring conformation in Escherichia coli cytosol obtained by cryo electron tomography | ||||||
Components |
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Keywords | CHAPERONE / Chaperonin / Folding cage / proteostasis / heat shock / ATPase | ||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / protein folding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 13.6 Å | ||||||
Authors | Wagner, J. / Caravajal, A.I. / Beck, F. / Bracher, A. / Wan, W. / Bohn, S. / Koerner, R. / Baumeister, W. / Fernandez-Busnadiego, R. / Hartl, F.U. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2024 Title: Visualizing chaperonin function in situ by cryo-electron tomography Authors: Wagner, J. / Caravajal, A.I. / Beck, F. / Bracher, A. / Wan, W. / Bohn, S. / Koerner, R. / Baumeister, W. / Fernandez-Busnadiego, R. / Hartl, F.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qxv.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qxv.ent.gz | 1020.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qxv_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8qxv_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8qxv_validation.xml.gz | 228.1 KB | Display | |
Data in CIF | 8qxv_validation.cif.gz | 343.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qxv ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qxv | HTTPS FTP |
-Related structure data
Related structure data | 18738MC 8p4mC 8p4nC 8p4oC 8p4pC 8p4rC 8qxsC 8qxtC 8qxuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 21 molecules ABCDEFGHIJKLMNOPQRSTU
#1: Protein | Mass: 57260.504 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: groEL, groL, mopA, b4143, JW4103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6F5, chaperonin ATPase #2: Protein | Mass: 10400.938 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: groES, groS, mopB, b4142, JW4102 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6F9 |
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-Non-polymers , 5 types, 315 molecules
#3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-ADP / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: (GroEL)14(GroES)7 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 13.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6681 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 216 / Num. of volumes extracted: 125860 | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 960.25 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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