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Yorodumi- PDB-6ht7: Crystal structure of the WT human mitochondrial chaperonin (ADP:B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ht7 | ||||||
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Title | Crystal structure of the WT human mitochondrial chaperonin (ADP:BeF3)14 complex | ||||||
Components |
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Keywords | CHAPERONE / protein folding chaperonin | ||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase ...coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / sperm plasma membrane / B cell activation / B cell proliferation / apoptotic mitochondrial changes / DNA replication origin binding / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / chaperone cofactor-dependent protein refolding / response to unfolded protein / RHOG GTPase cycle / chaperone-mediated protein complex assembly / positive regulation of interferon-alpha production / clathrin-coated pit / protein folding chaperone / sperm midpiece / Mitochondrial protein degradation / T cell activation / isomerase activity / positive regulation of interleukin-12 production / response to cold / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / osteoblast differentiation / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-6 production / double-stranded RNA binding / positive regulation of type II interferon production / unfolded protein binding / p53 binding / positive regulation of T cell activation / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / early endosome / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Jebara, F. / Patra, M. / Azem, A. / Hirsch, J. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Crystal structure of the WT human mitochondrial football Hsp60-Hsp10(ADPBeFx)14 complex Authors: Jebara, F. / Patra, M. / Azem, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ht7.cif.gz | 4.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ht7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ht7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ht7_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 6ht7_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 6ht7_validation.xml.gz | 175 KB | Display | |
Data in CIF | 6ht7_validation.cif.gz | 264.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/6ht7 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/6ht7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 28 molecules JIHNMLKGFEDCBAXWV21ZYUTSRQPO
#1: Protein | Mass: 58178.844 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPD1, HSP60 / Production host: Escherichia coli (E. coli) / References: UniProt: P10809, EC: 3.6.4.9 #2: Protein | Mass: 10946.674 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61604 |
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-Non-polymers , 4 types, 56 molecules
#3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-BEF / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-K / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, potassium chloride, HEPES sodium. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→48.95 Å / Num. obs: 144762 / % possible obs: 98.7 % / Redundancy: 4.1 % / Net I/σ(I): 6.95 |
Reflection shell | Resolution: 3.7→3.82 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→48.95 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 3.7→48.95 Å
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