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Yorodumi- PDB-7klu: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7klu | |||||||||||||||||||||
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Title | Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP | |||||||||||||||||||||
Components |
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Keywords | CHAPERONE / Hsp90 / TRAP1 / SdhB / mitochondria / SpyTag / SpyCatcher | |||||||||||||||||||||
Function / homology | Function and homology information translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Maturation of TCA enzymes and regulation of TCA cycle / tumor necrosis factor receptor binding ...translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Maturation of TCA enzymes and regulation of TCA cycle / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / 3 iron, 4 sulfur cluster binding / ubiquinone binding / Respiratory electron transport / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / tricarboxylic acid cycle / respiratory electron transport chain / proton motive force-driven mitochondrial ATP synthesis / cell periphery / ATP-dependent protein folding chaperone / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / unfolded protein binding / protein folding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Liu, Y.X. / Agard, D.A. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: To Be Published Title: Cryo-EM analysis of human mitochondrial Hsp90 in multiple tetrameric states Authors: Liu, Y.X. / Agard, D.A. / Elnatan, D. / Sun, M. / Larson, A.G. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7klu.cif.gz | 468.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7klu.ent.gz | 367.6 KB | Display | PDB format |
PDBx/mmJSON format | 7klu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7klu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7klu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7klu_validation.xml.gz | 72.6 KB | Display | |
Data in CIF | 7klu_validation.cif.gz | 108.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/7klu ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7klu | HTTPS FTP |
-Related structure data
Related structure data | 22918MC 7klvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 87094.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: TRAP1, HSP75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931 #2: Protein | Mass: 93121.344 Da / Num. of mol.: 2 Fragment: TRAP-1 (UNP residues 60-704) + SpyTag + SdhB (UNP residues 29-160) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: TRAP1, HSP75, SDHB, SDH, SDH1 / Production host: Escherichia coli (E. coli) References: UniProt: Q12931, UniProt: P21912, succinate dehydrogenase #3: Chemical | ChemComp-ANP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.360 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 66 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software | Name: CTFFIND / Category: CTF correction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94355 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6XG6 Accession code: 6XG6 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.41 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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