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- EMDB-54902: ADP-bound human mitochondrial Hsp60 single ring complex (C7) -

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Basic information

Entry
Database: EMDB / ID: EMD-54902
TitleADP-bound human mitochondrial Hsp60 single ring complex (C7)
Map data
Sample
  • Complex: ADP-bound mitocondrial Hsp60 chaperonin single-ring complex
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsmitochondrial / C7-symmetry / CHAPERONE
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 / negative regulation of execution phase of apoptosis / Mitochondrial protein import / positive regulation of macrophage activation / chaperonin ATPase / apoptotic mitochondrial changes / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / biological process involved in interaction with symbiont / B cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / B cell activation / DNA replication origin binding / apolipoprotein binding / response to unfolded protein / positive regulation of execution phase of apoptosis / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / positive regulation of interleukin-12 production / response to cold / clathrin-coated pit / Mitochondrial protein degradation / secretory granule / ATP-dependent protein folding chaperone / T cell activation / protein maturation / lipopolysaccharide binding / positive regulation of interleukin-6 production / positive regulation of T cell activation / positive regulation of type II interferon production / p53 binding / : / sperm midpiece / double-stranded RNA binding / single-stranded DNA binding / protein refolding / protein-folding chaperone binding / protein folding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / : / 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: 2.91 Å
AuthorsLopez-Alonso JP / Tascon I / Ubarretxena-Belandia I
Funding support Spain, 1 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-143177NB-I00 Spain
CitationJournal: To Be Published
Title: Structural remodeling of the mitochondrial protein biogenesis machinery upon proteostatic stress
Authors: Ehses K / Lopez-Alonso JP / Gonzalez A / Tascon I / Ubarretxena-Belandia I / Fernandez-Busnadiego R
History
DepositionAug 27, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54902.png

Downloads & links

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Map

FileDownload / File: emd_54902.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.52 Å		0.82 Å/pix.
x 400 pix.
= 329.52 Å		0.82 Å/pix.
x 400 pix.
= 329.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8238 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-1.4481221 - 2.08657
Average (Standard dev.)0.0005423834 (±0.034663692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54902_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54902_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54902_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ADP-bound mitocondrial Hsp60 chaperonin single-ring complex

EntireName: ADP-bound mitocondrial Hsp60 chaperonin single-ring complex
Components
  • Complex: ADP-bound mitocondrial Hsp60 chaperonin single-ring complex
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: ADP-bound mitocondrial Hsp60 chaperonin single-ring complex

SupramoleculeName: ADP-bound mitocondrial Hsp60 chaperonin single-ring complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 56.134441 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSAKDVKFGA DARALMLQGV DLLADAVAVT MGPKGRTVII EQSWGSPKVT KDGVTVAKSI DLKDKYKNIG AKLVQDVANN TNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG N IISDAMKK ...String:
GSAKDVKFGA DARALMLQGV DLLADAVAVT MGPKGRTVII EQSWGSPKVT KDGVTVAKSI DLKDKYKNIG AKLVQDVANN TNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG N IISDAMKK VGRKGVITVK DGKTLNDELE IIEGMKFDRG YISPYFINTS KGQKCEFQDA YVLLSEKKIS SIQSIVPALE IA NAHRKPL VIIAEDVDGE ALSTLVLNRL KVGLQVVAVK APGFGDNRKN QLKDMAIATG GAVFGEEGLT LNLEDVQPHD LGK VGEVIV TKDDAMLLKG KGDKAQIEKR IQEIIEQLDV TTSEYEKEKL NERLAKLSDG VAVLKVGGTS DVEVNEKKDR VTDA LNATR AAVEEGIVLG GGCALLRCIP ALDSLTPANE DQKIGIEIIK RTLKIPAMTI AKNAGVEGSL IVEKIMQSSS EVGYD AMAG DFVNMVEKGI IDPTKVVRTA LLDAAGVASL LTTAEVVVTE IPK

UniProtKB: 60 kDa heat shock protein, mitochondrial

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 7 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.7
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH3ClTris-HCl
20.0 mMKClpotassium chloride
10.0 mMMgCl2magnesium chloride
2.0 mMC10H16N5O13P3ATP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP
Details10 uM Hsp60

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 6 / Number real images: 100101 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 16.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 12338206
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 288807
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9es1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9shk:
ADP-bound human mitochondrial Hsp60 single ring complex (C7)

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