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- PDB-7azp: Structure of the human mitochondrial HSPD1 single ring -

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Basic information

Entry
Database: PDB / ID: 7azp
TitleStructure of the human mitochondrial HSPD1 single ring
Components60 kDa heat shock protein, mitochondrial
KeywordsCHAPERONE / HSPD1 / Hsp60 / chaperonin
Function / homology
Function and homology information


coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / apoptotic mitochondrial changes / sperm plasma membrane / B cell activation / positive regulation of interferon-alpha production / B cell proliferation / positive regulation of interleukin-10 production / positive regulation of execution phase of apoptosis / DNA replication origin binding / apolipoprotein binding / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / positive regulation of interleukin-12 production / Mitochondrial protein degradation / protein maturation / response to cold / T cell activation / secretory granule / isomerase activity / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of T cell activation / positive regulation of type II interferon production / p53 binding / unfolded protein binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
60 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKlebl, D.P. / Feasey, M.C. / Muench, S.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P026397/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: 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
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 60 kDa heat shock protein, mitochondrial
B: 60 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)408,1497
Polymers408,1497
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17030 Å2
ΔGint-98 kcal/mol
Surface area157410 Å2
MethodPISA

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Components

#1: Protein
60 kDa heat shock protein, mitochondrial / 60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / Hsp60 / HuCHA60 / Mitochondrial ...60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / Hsp60 / HuCHA60 / Mitochondrial matrix protein P1 / P60 lymphocyte 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
SpecimenConc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage 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

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
7UCSF Chimeramodel fitting
8Cootmodel fitting
9ISOLDEmodel fitting
11PHENIXmodel refinement
12RELIONinitial Euler assignment
13RELIONfinal Euler assignment
15RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124784 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11XCK

1xck

11XCK1PDBexperimental model
24PJ1

4pj1

14PJ12PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327615
ELECTRON MICROSCOPYf_angle_d0.52137261
ELECTRON MICROSCOPYf_dihedral_angle_d4.8143829
ELECTRON MICROSCOPYf_chiral_restr0.0424564
ELECTRON MICROSCOPYf_plane_restr0.0044802

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