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- PDB-9es6: ADP:BeF3-bound human mitochondrial Hsp60 double-ring complex -

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Basic information

Entry
Database: PDB / ID: 9es6
TitleADP:BeF3-bound human mitochondrial Hsp60 double-ring complex
Components60 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 / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / : / 60 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLopez-Alonso, J.P. / Tascon, I. / Ubarretxena-Belandia, I. / Shkolnisky, Y.
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
B: 60 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial
H: 60 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
M: 60 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)822,29670
Polymers814,50414
Non-polymers7,79356
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area64020 Å2
ΔGint-455 kcal/mol
Surface area166190 Å2
MethodPISA

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Components

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Protein , 1 types, 14 molecules ABCDEFGHIJKLMN

#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

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Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 140 / 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: ADP:BeF3-bound mitochondrial Hsp60 chaperonin double-ring complex
Type: COMPLEX / Entity ID: #1 / 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 mMTrisHCl(HOCH2)3CNH3Cl1
220 mMpotassium chlorideKCl1
310 mMmagnesium chlorideMgCl21
42 mMberyllium sulfateBeSO41
510 mMsodium fluorideNaF1
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
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4916
Image scansMovie frames/image: 60

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2Leginonimage acquisition
4RELION3CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 426391
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53971 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002535364
ELECTRON MICROSCOPYf_angle_d0.545647810
ELECTRON MICROSCOPYf_chiral_restr0.04125978
ELECTRON MICROSCOPYf_plane_restr0.00376048
ELECTRON MICROSCOPYf_dihedral_angle_d6.43275054

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