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- EMDB-19931: ATP-bound human mitochondrial Hsp60-Hsp10 half football complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19931
TitleATP-bound human mitochondrial Hsp60-Hsp10 half football complex
Map data
Sample
  • Complex: ATP-bound mitocondrial 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'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM 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 / 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 / RHOG GTPase cycle / 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 folding chaperone / intrinsic apoptotic signaling pathway / 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 / 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 / protein-containing complex / ATP hydrolysis activity / 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: 2.95 Å
AuthorsLopez-Alonso JP / Tascon I / Ubarretxena-Belandia I
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 Spain
CitationJournal: To Be Published
Title: Structural basis for ATP-triggered assembly of human mitochondrial Hsp60-Hsp10 chaperonin
Authors: Tascon I / Lopez-Alonso JP / Ubarretxena-Belandia I / Vilchez J / Shkolnisky Y / Azem A / Hirsch J
History
DepositionMar 25, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19931.png

Downloads & links

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Map

FileDownload / File: emd_19931.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: 0.221
Minimum - Maximum-0.6891077 - 1.080814
Average (Standard dev.)0.0010704068 (±0.032897886)
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_19931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19931_half_map_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_19931_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 : ATP-bound mitocondrial Hsp60-Hsp10 chaperonin half-football complex

EntireName: ATP-bound mitocondrial Hsp60-Hsp10 chaperonin half-football complex
Components
  • Complex: ATP-bound mitocondrial 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'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: ATP-bound mitocondrial Hsp60-Hsp10 chaperonin half-football complex

SupramoleculeName: ATP-bound mitocondrial 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'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2624 / 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 R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8114 / Average electron dose: 50.979 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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: 1085774
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 140572
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6mrc


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

PDB-9es1:
ATP-bound human mitochondrial Hsp60-Hsp10 half football complex

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