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- EMDB-19935: ADP:BeF3-bound human mitochondrial Hsp60-Hsp10 half-football complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19935
TitleADP:BeF3-bound human mitochondrial Hsp60-Hsp10 half-football complex
Map data
Sample
  • Complex: ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football complex
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial
    • Protein or peptide: 10 kDa heat shock protein, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
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 / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / biological process involved in interaction with symbiont / sperm plasma membrane / apoptotic mitochondrial changes / : / B cell activation / B cell proliferation / positive regulation of interferon-alpha production / DNA replication origin binding / positive regulation of interleukin-10 production / apolipoprotein binding / RHOG GTPase cycle / positive regulation of execution phase of apoptosis / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / sperm midpiece / clathrin-coated pit / positive regulation of interleukin-12 production / protein folding chaperone / Mitochondrial protein degradation / intrinsic apoptotic signaling pathway / response to cold / secretory granule / T cell activation / protein maturation / ATP-dependent protein folding chaperone / lipopolysaccharide binding / positive regulation of T cell activation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / osteoblast differentiation / 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 / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / 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 / GroES-like superfamily
Similarity search - Domain/homology
60 kDa heat shock protein, mitochondrial / 10 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLopez-Alonso JP / Tascon I / Ubarretxena-Belandia I / Shkolnisky Y
Funding support United States, Spain, 3 items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF) United States
Spanish Ministry of Science, Innovation, and Universities Spain
Other government
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis for ATP-driven double-ring assembly of the human mitochondrial Hsp60 chaperonin.
Authors: Igor Tascón / Jorge P López-Alonso / Yoel Shkolnisky / David Gil-Cartón / Jesús Vilchez-Garcia / Alberto G Berruezo / Yacob Gómez-Llorente / Radhika Malik / Fady Jebara / Malay Patra / ...Authors: Igor Tascón / Jorge P López-Alonso / Yoel Shkolnisky / David Gil-Cartón / Jesús Vilchez-Garcia / Alberto G Berruezo / Yacob Gómez-Llorente / Radhika Malik / Fady Jebara / Malay Patra / Joel A Hirsch / Abdussalam Azem / Iban Ubarretxena-Belandia
Abstract: The ATP-driven mHsp60:mHsp10 chaperonin system assists protein folding within the mitochondrial matrix of human cells. Substrate protein folding has been proposed to occur through interconnected ...The ATP-driven mHsp60:mHsp10 chaperonin system assists protein folding within the mitochondrial matrix of human cells. Substrate protein folding has been proposed to occur through interconnected single- and double-ring pathways. In the absence of nucleotide, mHsp60 exists in equilibrium between free protomers and heptameric single rings, while the formation of double rings requires ATP. Here, we present cryo-electron microscopy structures of mHsp60 in the apo state, bound to ATP, and bound to ATP in complex with the cochaperonin mHsp10. ATP binding to single-ring apo mHsp60 triggers coordinated conformational changes in the intermediate and apical domains, resulting in a highly dynamic apical region within the ring. Extensive inter-subunit rearrangements flatten the equatorial surface of each ring, thereby enabling inter-ring contacts that stitch the rings together to form double-ring mHsp60 . Collectively, these structures define the structural basis of ATP-driven double-ring assembly of a human mitochondrial chaperonin responsible for maintaining mitochondrial protein homeostasis.
History
DepositionMar 25, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19935.png

Downloads & links

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Map

FileDownload / File: emd_19935.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 336 pix.
= 360.612 Å		1.07 Å/pix.
x 336 pix.
= 360.612 Å		1.07 Å/pix.
x 336 pix.
= 360.612 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0206
Minimum - Maximum-0.041853763 - 0.09448153
Average (Standard dev.)0.00017597964 (±0.0023814205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 360.61203 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19935_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_19935_half_map_1.map
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Half map: #1

Fileemd_19935_half_map_2.map
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Sample components

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Entire : ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football...

EntireName: ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football complex
Components
  • Complex: ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football complex
    • Protein or peptide: 60 kDa heat shock protein, mitochondrial
    • Protein or peptide: 10 kDa heat shock protein, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football...

SupramoleculeName: ADP:BeF3-bound mitochondrial Hsp60-Hsp10 chaperonin half-football complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: ec: 3.6.4.9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.178844 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 IPKEEKDPGM GAMGGMGGGM GGGMF

UniProtKB: 60 kDa heat shock protein, mitochondrial

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Macromolecule #2: 10 kDa heat shock protein, mitochondrial

MacromoleculeName: 10 kDa heat shock protein, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.946674 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGQAFRKFL PLFDRVLVER SAAETVTKGG IMLPEKSQGK VLQATVVAVG SGSKGKGGEI QPVSVKVGDK VLLPEYGGTK VVLDDKDYF LFRDGDILGK YVD

UniProtKB: 10 kDa heat shock protein, mitochondrial

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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 #4: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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)3CNH3ClTrisHCl
20.0 mMKClpotassium chloride
10.0 mMMgCl2magnessium chloride
2.0 mMBeSO4beryllium sulfate
10.0 mMNaFsodium fluoride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3335 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 373505
CTF correctionSoftware - Name: RELION (ver. 3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied 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. 3.0) / Number images used: 18636
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9es5:
ADP:BeF3-bound human mitochondrial Hsp60-Hsp10 half-football complex

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