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- PDB-9es0: ATP-bound human mitochondrial Hsp60-Hsp10 football complex -

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Basic information

Entry
Database: PDB / ID: 9es0
TitleATP-bound human mitochondrial Hsp60-Hsp10 football complex
Components
  • 10 kDa heat shock protein, mitochondrial
  • 60 kDa heat shock protein, mitochondrial
KeywordsCHAPERONE / mitochondrial / D7-symmetry
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 / biological process involved in interaction with symbiont / 'de novo' protein folding / sperm plasma membrane / apoptotic mitochondrial changes / B cell activation / B cell proliferation / : / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / DNA replication origin binding / 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 / T cell activation / secretory granule / protein maturation / lipopolysaccharide binding / ATP-dependent protein folding chaperone / 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 / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
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
ADENOSINE-5'-TRIPHOSPHATE / : / 60 kDa heat shock protein, mitochondrial / 10 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLopez-Alonso, J.P. / Tascon, I. / Ubarretxena-Belandia, I.
Funding support United States, Spain, 3items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF) United States
Spanish Ministry of Science, Innovation, and Universities Spain
Other government
CitationJournal: To Be Published
Title: Structural basis for ATP-triggered assembly of human mitochondrial Hsp60-Hsp10 chaperonin
Authors: Tascon, I. / Lopez-Alonso, J.P. / Ubarretxena-Belandia, I. / Vilchez, J. / Shkolnisky, Y. / Azem, A. / Hirsch, J.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60 kDa heat shock protein, mitochondrial
a: 10 kDa heat shock protein, mitochondrial
B: 60 kDa heat shock protein, mitochondrial
b: 10 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
c: 10 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
d: 10 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
e: 10 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
f: 10 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial
g: 10 kDa heat shock protein, mitochondrial
H: 60 kDa heat shock protein, mitochondrial
h: 10 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
i: 10 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
j: 10 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
k: 10 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
l: 10 kDa heat shock protein, mitochondrial
M: 60 kDa heat shock protein, mitochondrial
m: 10 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial
n: 10 kDa heat shock protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)975,74570
Polymers967,75728
Non-polymers7,98842
Water80,2574455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area104750 Å2
ΔGint-710 kcal/mol
Surface area347120 Å2
MethodPISA

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Components

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Protein , 2 types, 28 molecules ABCDEFGHIJKLMNabcdefghijklmn

#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: 58178.844 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPD1, HSP60 / Production host: Escherichia coli (E. coli) / References: UniProt: P10809, EC: 3.6.4.9
#2: Protein
10 kDa heat shock protein, mitochondrial / Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF


Mass: 10946.674 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61604

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Non-polymers , 4 types, 4497 molecules

#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: ATP-bound mitocondrial Hsp60-Hsp10 chaperonin football complex
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl(HOCH2)3CNH3Cl1
220 mMpotassium chlorideKCl1
310 mMmagnesium chlorideMgCl21
42 mMATPC10H16N5O13P31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 %

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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 / Nominal magnification: 105000 X / Nominal defocus max: 16000 nm / Nominal defocus min: 8000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.979 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8114

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2EPUimage acquisition
4cryoSPARC3.3.1CTF correction
7UCSF Chimera1.16model fitting
9PHENIX1.20.1model refinement
10Coot0.9.1model refinement
11cryoSPARC3.3.1initial Euler assignment
12cryoSPARC3.3.1final Euler assignment
13cryoSPARC3.3.1classification
14cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1085774
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198830 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6MRC

6mrc


Accession code: 6MRC / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002966626
ELECTRON MICROSCOPYf_angle_d0.581189908
ELECTRON MICROSCOPYf_chiral_restr0.045410836
ELECTRON MICROSCOPYf_plane_restr0.004611494
ELECTRON MICROSCOPYf_dihedral_angle_d5.12959212

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