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- PDB-7l7s: Human mitochondrial chaperonin mHsp60 -

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Basic information

Entry
Database: PDB / ID: 7l7s
TitleHuman mitochondrial chaperonin mHsp60
Components60 kDa heat shock protein, mitochondrial
KeywordsCHAPERONE / ISOMERASE / mHsp60 / GroEL / 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 / 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 / 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 / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / sperm plasma membrane / 'de novo' protein folding / B cell proliferation / DNA replication origin binding / B cell activation / positive regulation of interferon-alpha production / apoptotic mitochondrial changes / positive regulation of interleukin-10 production / apolipoprotein binding / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / Mitochondrial protein degradation / positive regulation of interleukin-12 production / 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 type II interferon production / positive regulation of T cell activation / double-stranded RNA binding / unfolded protein binding / p53 binding / 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 / 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
AuthorsChen, L. / Wang, J.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129539 United States
CitationJournal: Sci Rep / Year: 2021
Title: Structural basis for the structural dynamics of human mitochondrial chaperonin mHsp60.
Authors: Joseph Che-Yen Wang / Lingling Chen /
Abstract: Human mitochondrial chaperonin mHsp60 is essential for mitochondrial function by assisting folding of mitochondrial proteins. Unlike the double-ring bacterial GroEL, mHsp60 exists as a heptameric ...Human mitochondrial chaperonin mHsp60 is essential for mitochondrial function by assisting folding of mitochondrial proteins. Unlike the double-ring bacterial GroEL, mHsp60 exists as a heptameric ring that is unstable and dissociates to subunits. The structural dynamics has been implicated for a unique mechanism of mHsp60. We purified active heptameric mHsp60, and determined a cryo-EM structure of mHsp60 heptamer at 3.4 Å. Of the three domains, the equatorial domains contribute most to the inter-subunit interactions, which include a four-stranded β sheet. Our structural comparison with GroEL shows that mHsp60 contains several unique sequences that directly decrease the sidechain interactions around the β sheet and indirectly shorten β strands by disengaging the backbones of the flanking residues from hydrogen bonding in the β strand conformation. The decreased inter-subunit interactions result in a small inter-subunit interface in mHsp60 compared to GroEL, providing a structural basis for the dynamics of mHsp60 subunit association. Importantly, the unique sequences are conserved among higher eukaryotic mitochondrial chaperonins, suggesting the importance of structural dynamics for eukaryotic chaperonins. Our structural comparison with the single-ring mHsp60-mHsp10 shows that upon mHsp10 binding the shortened inter-subunit β sheet is restored and the overall inter-subunit interface of mHsp60 increases drastically. Our structural basis for the mHsp10 induced stabilization of mHsp60 subunit interaction is consistent with the literature that mHsp10 stabilizes mHsp60 quaternary structure. Together, our studies provide structural bases for structural dynamics of the mHsp60 heptamer and for the stabilizing effect of mHsp10 on mHsp60 subunit association.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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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  • Deposited structure unit
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  • EMDB-23217
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 60 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
M: 60 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)391,0287
Polymers391,0287
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, We used size-exclusion chromatography (SEC) and dynamic light scattering (DLS) to compare mHsp60 with the double-ring GroEL and single-ring GroEL, microscopy, We used ...Evidence: light scattering, We used size-exclusion chromatography (SEC) and dynamic light scattering (DLS) to compare mHsp60 with the double-ring GroEL and single-ring GroEL, microscopy, We used negative stain TEM and cryo-EM to confirm the assembly
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 55861.137 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(DE3) (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 chaperonin mHsp60 in a heptameric ring conformation
Type: COMPLEX
Details: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.060 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21DE3
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
210 mMKHepes1
31 mMEDTA1
41 mMDTT1
55 %glycerol1
SpecimenConc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample is monodisperse
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imaged
1144GATAN K3 BIOQUANTUM (6k x 4k)1
2153GATAN K3 (6k x 4k)3
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryDetailsImage processing-ID
1EMAN22.31particle selectione2boxer.py1
2EPUimage acquisition
3Leginonimage acquisition
5GctfCTF correction1
8UCSF Chimera1.15model fitting
10RELION3.1initial Euler assignment1
11RELION3.1final Euler assignment1
13RELION3.13D reconstruction1
14EMAN22.31particle selection2
16CTFFIND4CTF correction2
17RELION3.1initial Euler assignment2
18RELION3.1final Euler assignment2
20RELION3.13D reconstruction2
21PHENIX3965model refinement
Image processing
IDImage recording-ID
11
22
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
IDImage processing-IDEntry-IDPoint symmetry
117L7SC7 (7 fold cyclic)
227L7SC7 (7 fold cyclic)
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.5FSC 0.143 CUT-OFF19606017L7SPOINT
23.5FSC 0.143 CUT-OFF18260027L7SPOINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 1PCQ / Initial refinement model-ID: 1 / Pdb chain residue range: 2-525 / PDB-ID: 1PCQ

1pcq

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1H
2I
3J
4K
5L
6M
7N
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00727580
ELECTRON MICROSCOPYf_angle_d0.69937205
ELECTRON MICROSCOPYf_dihedral_angle_d18.38510500
ELECTRON MICROSCOPYf_chiral_restr0.0454557
ELECTRON MICROSCOPYf_plane_restr0.0044795

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