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Open data
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Basic information
Entry | Database: PDB / ID: 7azp | |||||||||
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Title | Structure of the human mitochondrial HSPD1 single ring | |||||||||
![]() | 60 kDa heat shock protein, mitochondrial | |||||||||
![]() | CHAPERONE / HSPD1 / Hsp60 / chaperonin | |||||||||
Function / homology | ![]() 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 / response to unfolded protein / chaperone-mediated protein complex assembly / positive regulation of interferon-alpha production / clathrin-coated pit / sperm midpiece / Mitochondrial protein degradation / isomerase activity / T cell activation / positive regulation of interleukin-12 production / response to cold / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / 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 / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Klebl, D.P. / Feasey, M.C. / Muench, S.P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of human mitochondrial HSPD1. Authors: David P Klebl / Matthew C Feasey / Emma L Hesketh / Neil A Ranson / Heiko Wurdak / Frank Sobott / Robin S Bon / Stephen P Muench / ![]() ![]() Abstract: Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these ...Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these proteins. In comparison, its human homolog, known as mitochondrial heat shock protein family member D1 (HSPD1) is poorly understood. Here, we present the structure of HSPD1 in the apo state determined by cryo-electron microscopy (cryo-EM). Unlike GroEL, HSPD1 forms mostly single ring assemblies in the absence of co-chaperonin (HSPE1). Comparison with GroEL shows a rotation and increased flexibility of the apical domain. Together with published structures of the HSPD1/HSPE1 co-chaperonin complex, this work gives insight into the structural changes that occur during the catalytic cycle. This new understanding of HSPD1 structure and its rearrangements upon complex formation may provide new insights for the development of HSPD1-targeting treatments against a diverse range of diseases including glioblastoma. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 585.5 KB | Display | ![]() |
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PDB format | ![]() | 491.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 102.9 KB | Display | |
Data in CIF | ![]() | 155.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11950MC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 58306.977 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: human mitochondrial heat shock protein family member D1 (HSPD1) Type: COMPLEX Details: produced by heterologous expression, mature HSPD1, apo state Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.7 |
Specimen | Conc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: blot time 6 s blot force 6 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 70 sec. / Electron dose: 38.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124784 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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