[English] 日本語
Yorodumi
- PDB-6mrc: ADP-bound human mitochondrial Hsp60-Hsp10 football complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mrc
TitleADP-bound human mitochondrial Hsp60-Hsp10 football complex
Components
  • 10 kDa heat shock protein, mitochondrial
  • 60 kDa heat shock protein, mitochondrial
KeywordsCHAPERONE / Complex / ADP / Football
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 / 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 / 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
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family ...10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / 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 / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 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: 3.08 Å
AuthorsGomez-Llorente, Y. / Jebara, F. / Patra, M. / Malik, R. / Nissemblat, S. / Azem, A. / Hirsch, J.A. / Ubarretxena-Belandia, I.
Funding support United States, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin.
Authors: Yacob Gomez-Llorente / Fady Jebara / Malay Patra / Radhika Malik / Shahar Nisemblat / Orna Chomsky-Hecht / Avital Parnas / Abdussalam Azem / Joel A Hirsch / Iban Ubarretxena-Belandia /
Abstract: mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF- ...mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF-bound) ground-state mimic double-ring mHsp60-(mHsp10) football complex, and the cryo-EM structures of the ADP-bound successor mHsp60-(mHsp10) complex, and a single-ring mHsp60-mHsp10 half-football. The structures explain the nucleotide dependence of mHsp60 ring formation, and reveal an inter-ring nucleotide symmetry consistent with the absence of negative cooperativity. In the ground-state a two-fold symmetric H-bond and a salt bridge stitch the double-rings together, whereas only the H-bond remains as the equatorial gap increases in an ADP football poised to split into half-footballs. Refolding assays demonstrate obligate single- and double-ring mHsp60 variants are active, and complementation analysis in bacteria shows the single-ring variant is as efficient as wild-type mHsp60. Our work provides a structural basis for active single- and double-ring complexes coexisting in the mHsp60-mHsp10 chaperonin reaction cycle.
History
DepositionOct 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Structure summary / Category: audit_author
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9195
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 60 kDa heat shock protein, mitochondrial
V: 10 kDa heat shock protein, mitochondrial
2: 10 kDa heat shock protein, mitochondrial
1: 10 kDa heat shock protein, mitochondrial
Z: 10 kDa heat shock protein, mitochondrial
Y: 10 kDa heat shock protein, mitochondrial
X: 10 kDa heat shock protein, mitochondrial
W: 10 kDa heat shock protein, mitochondrial
R: 10 kDa heat shock protein, mitochondrial
Q: 10 kDa heat shock protein, mitochondrial
P: 10 kDa heat shock protein, mitochondrial
O: 10 kDa heat shock protein, mitochondrial
U: 10 kDa heat shock protein, mitochondrial
T: 10 kDa heat shock protein, mitochondrial
S: 10 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial
M: 60 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
B: 60 kDa heat shock protein, mitochondrial
A: 60 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)944,43356
Polymers938,11128
Non-polymers6,32128
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area97650 Å2
ΔGint-691 kcal/mol
Surface area357680 Å2

-
Components

#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: 56263.559 Da / Num. of mol.: 14 / Fragment: UNP residues 27-552
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: 10744.400 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
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of Hsp60 with Hsp10 bound to ADP and Mg / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.98 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Homemade
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

-
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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 63 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4CTFFINDCTF correction
8PHENIXmodel refinement
10RELIONinitial Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66013 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00469650
ELECTRON MICROSCOPYf_angle_d0.8796796
ELECTRON MICROSCOPYf_dihedral_angle_d6.83741608
ELECTRON MICROSCOPYf_chiral_restr0.06810850
ELECTRON MICROSCOPYf_plane_restr0.00411774

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more