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- EMDB-23217: Human mitochondrial chaperonin mHsp60 -

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Basic information

Entry
Database: EMDB / ID: EMD-23217
TitleHuman mitochondrial chaperonin mHsp60
Map dataCryo-EM structure of mHsp60
Sample
  • Complex: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial
KeywordsmHsp60 / GroEL / chaperonin / CHAPERONE / ISOMERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen L / Wang JCY
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l7s
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23217.png

Downloads & links

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Map

FileDownload / File: emd_23217.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mHsp60
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.17286505 - 0.25358173
Average (Standard dev.)0.000010617483 (±0.007372357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1730.2540.000

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Supplemental data

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Sample components

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Entire : Human mitochondrial chaperonin mHsp60 in a heptameric ring confor...

EntireName: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
Components
  • Complex: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial

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Supramolecule #1: Human mitochondrial chaperonin mHsp60 in a heptameric ring confor...

SupramoleculeName: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: 60 kDa heat shock protein, mitochondrial

MacromoleculeName: 60 kDa heat shock protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.861137 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AKDVKFGADA RALMLQGVDL LADAVAVTMG PKGRTVIIEQ SWGSPKVTKD GVTVAKSIDL KDKYKNIGAK LVQDVANNTN EEAGDGTTT ATVLARSIAK EGFEKISKGA NPVEIRRGVM LAVDAVIAEL KKQSKPVTTP EEIAQVATIS ANGDKEIGNI I SDAMKKVG ...String:
AKDVKFGADA RALMLQGVDL LADAVAVTMG PKGRTVIIEQ SWGSPKVTKD GVTVAKSIDL KDKYKNIGAK LVQDVANNTN EEAGDGTTT ATVLARSIAK EGFEKISKGA NPVEIRRGVM LAVDAVIAEL KKQSKPVTTP EEIAQVATIS ANGDKEIGNI I SDAMKKVG RKGVITVKDG KTLNDELEII EGMKFDRGYI SPYFINTSKG QKCEFQDAYV LLSEKKISSI QSIVPALEIA NA HRKPLVI IAEDVDGEAL STLVLNRLKV GLQVVAVKAP GFGDNRKNQL KDMAIATGGA VFGEEGLTLN LEDVQPHDLG KVG EVIVTK DDAMLLKGKG DKAQIEKRIQ EIIEQLDVTT SEYEKEKLNE RLAKLSDGVA VLKVGGTSDV EVNEKKDRVT DALN ATRAA VEEGIVLGGG CALLRCIPAL DSLTPANEDQ KIGIEIIKRT LKIPAMTIAK NAGVEGSLIV EKIMQSSSEV GYDAM AGDF VNMVEKGIID PTKVVRTALL DAAGVASLLT TAEVVVTEIP

UniProtKB: 60 kDa heat shock protein, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
10.0 mMKHepes
1.0 mMEDTA
1.0 mMDTT
5.0 %glycerol
GridModel: Quantifoil / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GOLD / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsThe sample is monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Average electron dose: 44.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 3 / #1 - Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
Startup modelType of model: OTHER / Details: RELION initial model building
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 196060
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
Startup modelType of model: OTHER / Details: RELION initial model building
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 182600
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1pcq

chain_id: H, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: I, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: J, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: K, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: L, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: M, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model

1pcq

chain_id: N, residue_range: 2-525, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7l7s:
Human mitochondrial chaperonin mHsp60

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