+Open data
-Basic information
Entry | Database: PDB / ID: 7azp | |||||||||
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Title | Structure of the human mitochondrial HSPD1 single ring | |||||||||
Components | 60 kDa heat shock protein, mitochondrial | |||||||||
Keywords | CHAPERONE / HSPD1 / Hsp60 / chaperonin | |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / 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 / DNA replication origin binding / B cell proliferation / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / isomerase activity / sperm midpiece / response to cold / positive regulation of interleukin-12 production / T cell activation / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of T cell activation / unfolded protein binding / positive regulation of type II interferon production / p53 binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / protein stabilization / early endosome / 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 / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Klebl, D.P. / Feasey, M.C. / Muench, S.P. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: iScience / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7azp.cif.gz | 585.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7azp.ent.gz | 491.2 KB | Display | PDB format |
PDBx/mmJSON format | 7azp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7azp ftp://data.pdbj.org/pub/pdb/validation_reports/az/7azp | HTTPS FTP |
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-Related structure data
Related structure data | 11950MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: HSPD1, HSP60 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P10809, chaperonin ATPase |
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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: 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: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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 |
-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 FIELDBright-field microscopy |
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 |
-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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