6HT7 | pdb_00006ht7

Crystal structure of the WT human mitochondrial chaperonin (ADP:BeF3)14 complex

PDB DOI: https://doi.org/10.2210/pdb6HT7/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-10-03 Released: 2020-04-29
Deposition Author(s): Jebara, F., Patra, M., Azem, A., Hirsch, J.
Funding Organization(s): United States - Israel Binational Science Foundation (BSF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.303 (DCC)
R-Value Work:
0.269 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the WT human mitochondrial football Hsp60-Hsp10(ADPBeFx)14 complex

Jebara, F., Patra, M., Azem, A.

(2020) Nat Commun

DOI: https://doi.org/10.1038/s41467-020-15698-8

Macromolecule Content

Total Structure Weight: 975.55 kDa
Atom Count: 66,038
Modeled Residue Count: 8,792
Deposited Residue Count: 9,114
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa heat shock protein, mitochondrial	A [auth J] AA [auth B] BA [auth A] I J [auth H] A [auth J], AA [auth B], BA [auth A], I, J [auth H], K [auth N], L [auth M], M [auth L], N [auth K], O [auth G], W [auth F], X [auth E], Y [auth D], Z [auth C]	549	Homo sapiens	Mutation(s): 0 Gene Names: HSPD1, HSP60 EC: 3.6.4.9 (PDB Primary Data), 5.6.1.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P10809 (Homo sapiens) Explore P10809 Go to UniProtKB: P10809
PHAROS: P10809 GTEx: ENSG00000144381
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10809
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10 kDa heat shock protein, mitochondrial	B [auth X] C [auth W] D [auth V] E [auth 2] F [auth 1] B [auth X], C [auth W], D [auth V], E [auth 2], F [auth 1], G [auth Z], H [auth Y], P [auth U], Q [auth T], R [auth S], S [auth R], T [auth Q], U [auth P], V [auth O]	102	Homo sapiens	Mutation(s): 0 Gene Names: HSPE1
UniProt & NIH Common Fund Data Resources
Find proteins for P61604 (Homo sapiens) Explore P61604 Go to UniProtKB: P61604
PHAROS: P61604 GTEx: ENSG00000115541
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61604
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain CA [auth J] SDF format, chain CC [auth A] SDF format, chain EB [auth G] SDF format, chain GA [auth I] SDF format, chain IB [auth F] SDF format, chain KA [auth H] SDF format, chain MB [auth E] SDF format, chain OA [auth N] SDF format, chain QB [auth D] SDF format, chain SA [auth M] SDF format, chain UB [auth C] SDF format, chain WA [auth L] SDF format, chain YB [auth B] MOL2 format, chain AB [auth K] MOL2 format, chain CA [auth J] MOL2 format, chain CC [auth A] MOL2 format, chain EB [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain IB [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain MB [auth E] MOL2 format, chain OA [auth N] MOL2 format, chain QB [auth D] MOL2 format, chain SA [auth M] MOL2 format, chain UB [auth C] MOL2 format, chain WA [auth L] MOL2 format, chain YB [auth B] mmCIF format, chain AB [auth K] mmCIF format, chain CA [auth J] mmCIF format, chain CC [auth A] mmCIF format, chain EB [auth G] mmCIF format, chain GA [auth I] mmCIF format, chain IB [auth F] mmCIF format, chain KA [auth H] mmCIF format, chain MB [auth E] mmCIF format, chain OA [auth N] mmCIF format, chain QB [auth D] mmCIF format, chain SA [auth M] mmCIF format, chain UB [auth C] mmCIF format, chain WA [auth L] mmCIF format, chain YB [auth B]	AB [auth K] CA [auth J] CC [auth A] EB [auth G] GA [auth I] AB [auth K], CA [auth J], CC [auth A], EB [auth G], GA [auth I], IB [auth F], KA [auth H], MB [auth E], OA [auth N], QB [auth D], SA [auth M], UB [auth C], WA [auth L], YB [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AB [auth K] Focus chain CA [auth J] Focus chain CC [auth A] Focus chain EB [auth G] Focus chain GA [auth I] Focus chain IB [auth F] Focus chain KA [auth H] Focus chain MB [auth E] Focus chain OA [auth N] Focus chain QB [auth D] Focus chain SA [auth M] Focus chain UB [auth C] Focus chain WA [auth L] Focus chain YB [auth B] Interactions & Density Focus chain AB [auth K] Focus chain CA [auth J] Focus chain CC [auth A] Focus chain EB [auth G] Focus chain GA [auth I] Focus chain IB [auth F] Focus chain KA [auth H] Focus chain MB [auth E] Focus chain OA [auth N] Focus chain QB [auth D] Focus chain SA [auth M] Focus chain UB [auth C] Focus chain WA [auth L] Focus chain YB [auth B]
BEF Query on BEF Download:Ideal Coordinates CCD File SDF format, chain BB [auth K] SDF format, chain DA [auth J] SDF format, chain DC [auth A] SDF format, chain FB [auth G] SDF format, chain HA [auth I] SDF format, chain JB [auth F] SDF format, chain LA [auth H] SDF format, chain NB [auth E] SDF format, chain PA [auth N] SDF format, chain RB [auth D] SDF format, chain TA [auth M] SDF format, chain VB [auth C] SDF format, chain XA [auth L] SDF format, chain ZB [auth B] MOL2 format, chain BB [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain DC [auth A] MOL2 format, chain FB [auth G] MOL2 format, chain HA [auth I] MOL2 format, chain JB [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain NB [auth E] MOL2 format, chain PA [auth N] MOL2 format, chain RB [auth D] MOL2 format, chain TA [auth M] MOL2 format, chain VB [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain ZB [auth B] mmCIF format, chain BB [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain DC [auth A] mmCIF format, chain FB [auth G] mmCIF format, chain HA [auth I] mmCIF format, chain JB [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain NB [auth E] mmCIF format, chain PA [auth N] mmCIF format, chain RB [auth D] mmCIF format, chain TA [auth M] mmCIF format, chain VB [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain ZB [auth B]	BB [auth K] DA [auth J] DC [auth A] FB [auth G] HA [auth I] BB [auth K], DA [auth J], DC [auth A], FB [auth G], HA [auth I], JB [auth F], LA [auth H], NB [auth E], PA [auth N], RB [auth D], TA [auth M], VB [auth C], XA [auth L], ZB [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain BB [auth K] Focus chain DA [auth J] Focus chain DC [auth A] Focus chain FB [auth G] Focus chain HA [auth I] Focus chain JB [auth F] Focus chain LA [auth H] Focus chain NB [auth E] Focus chain PA [auth N] Focus chain RB [auth D] Focus chain TA [auth M] Focus chain VB [auth C] Focus chain XA [auth L] Focus chain ZB [auth B] Interactions & Density Focus chain BB [auth K] Focus chain DA [auth J] Focus chain DC [auth A] Focus chain FB [auth G] Focus chain HA [auth I] Focus chain JB [auth F] Focus chain LA [auth H] Focus chain NB [auth E] Focus chain PA [auth N] Focus chain RB [auth D] Focus chain TA [auth M] Focus chain VB [auth C] Focus chain XA [auth L] Focus chain ZB [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain BC [auth B] SDF format, chain DB [auth K] SDF format, chain FA [auth J] SDF format, chain FC [auth A] SDF format, chain HB [auth G] SDF format, chain JA [auth I] SDF format, chain LB [auth F] SDF format, chain NA [auth H] SDF format, chain PB [auth E] SDF format, chain RA [auth N] SDF format, chain TB [auth D] SDF format, chain VA [auth M] SDF format, chain XB [auth C] SDF format, chain ZA [auth L] MOL2 format, chain BC [auth B] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain FC [auth A] MOL2 format, chain HB [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain LB [auth F] MOL2 format, chain NA [auth H] MOL2 format, chain PB [auth E] MOL2 format, chain RA [auth N] MOL2 format, chain TB [auth D] MOL2 format, chain VA [auth M] MOL2 format, chain XB [auth C] MOL2 format, chain ZA [auth L] mmCIF format, chain BC [auth B] mmCIF format, chain DB [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain FC [auth A] mmCIF format, chain HB [auth G] mmCIF format, chain JA [auth I] mmCIF format, chain LB [auth F] mmCIF format, chain NA [auth H] mmCIF format, chain PB [auth E] mmCIF format, chain RA [auth N] mmCIF format, chain TB [auth D] mmCIF format, chain VA [auth M] mmCIF format, chain XB [auth C] mmCIF format, chain ZA [auth L]	BC [auth B] DB [auth K] FA [auth J] FC [auth A] HB [auth G] BC [auth B], DB [auth K], FA [auth J], FC [auth A], HB [auth G], JA [auth I], LB [auth F], NA [auth H], PB [auth E], RA [auth N], TB [auth D], VA [auth M], XB [auth C], ZA [auth L]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BC [auth B] Focus chain DB [auth K] Focus chain FA [auth J] Focus chain FC [auth A] Focus chain HB [auth G] Focus chain JA [auth I] Focus chain LB [auth F] Focus chain NA [auth H] Focus chain PB [auth E] Focus chain RA [auth N] Focus chain TB [auth D] Focus chain VA [auth M] Focus chain XB [auth C] Focus chain ZA [auth L] Interactions & Density Focus chain BC [auth B] Focus chain DB [auth K] Focus chain FA [auth J] Focus chain FC [auth A] Focus chain HB [auth G] Focus chain JA [auth I] Focus chain LB [auth F] Focus chain NA [auth H] Focus chain PB [auth E] Focus chain RA [auth N] Focus chain TB [auth D] Focus chain VA [auth M] Focus chain XB [auth C] Focus chain ZA [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AC [auth B] SDF format, chain CB [auth K] SDF format, chain EA [auth J] SDF format, chain EC [auth A] SDF format, chain GB [auth G] SDF format, chain IA [auth I] SDF format, chain KB [auth F] SDF format, chain MA [auth H] SDF format, chain OB [auth E] SDF format, chain QA [auth N] SDF format, chain SB [auth D] SDF format, chain UA [auth M] SDF format, chain WB [auth C] SDF format, chain YA [auth L] MOL2 format, chain AC [auth B] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain EC [auth A] MOL2 format, chain GB [auth G] MOL2 format, chain IA [auth I] MOL2 format, chain KB [auth F] MOL2 format, chain MA [auth H] MOL2 format, chain OB [auth E] MOL2 format, chain QA [auth N] MOL2 format, chain SB [auth D] MOL2 format, chain UA [auth M] MOL2 format, chain WB [auth C] MOL2 format, chain YA [auth L] mmCIF format, chain AC [auth B] mmCIF format, chain CB [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain EC [auth A] mmCIF format, chain GB [auth G] mmCIF format, chain IA [auth I] mmCIF format, chain KB [auth F] mmCIF format, chain MA [auth H] mmCIF format, chain OB [auth E] mmCIF format, chain QA [auth N] mmCIF format, chain SB [auth D] mmCIF format, chain UA [auth M] mmCIF format, chain WB [auth C] mmCIF format, chain YA [auth L]	AC [auth B] CB [auth K] EA [auth J] EC [auth A] GB [auth G] AC [auth B], CB [auth K], EA [auth J], EC [auth A], GB [auth G], IA [auth I], KB [auth F], MA [auth H], OB [auth E], QA [auth N], SB [auth D], UA [auth M], WB [auth C], YA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AC [auth B] Focus chain CB [auth K] Focus chain EA [auth J] Focus chain EC [auth A] Focus chain GB [auth G] Focus chain IA [auth I] Focus chain KB [auth F] Focus chain MA [auth H] Focus chain OB [auth E] Focus chain QA [auth N] Focus chain SB [auth D] Focus chain UA [auth M] Focus chain WB [auth C] Focus chain YA [auth L] Interactions & Density Focus chain AC [auth B] Focus chain CB [auth K] Focus chain EA [auth J] Focus chain EC [auth A] Focus chain GB [auth G] Focus chain IA [auth I] Focus chain KB [auth F] Focus chain MA [auth H] Focus chain OB [auth E] Focus chain QA [auth N] Focus chain SB [auth D] Focus chain UA [auth M] Focus chain WB [auth C] Focus chain YA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.303 (DCC)
R-Value Work: 0.269 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.59	α = 90
b = 295.78	β = 90
c = 326.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
MxCuBE	data collection
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
United States - Israel Binational Science Foundation (BSF)	Israel	2015214

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2022-03-30
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.2: 2024-06-19
Changes: Data collection