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:
0.300 (DCC)
R-Value Work:
0.270 (DCC)

wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10809
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 MB [auth E] 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] SDF format, chain OA [auth N] SDF format, chain KA [auth H] 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 MB [auth E] 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] MOL2 format, chain OA [auth N] MOL2 format, chain KA [auth H] 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 MB [auth E] 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] mmCIF format, chain OA [auth N] mmCIF format, chain KA [auth H]	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 JB [auth F] SDF format, chain LA [auth H] 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] SDF format, chain PA [auth N] SDF format, chain NB [auth E] SDF format, chain HA [auth I] 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 JB [auth F] MOL2 format, chain LA [auth H] 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] MOL2 format, chain PA [auth N] MOL2 format, chain NB [auth E] MOL2 format, chain HA [auth I] 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 JB [auth F] mmCIF format, chain LA [auth H] 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] mmCIF format, chain PA [auth N] mmCIF format, chain NB [auth E] mmCIF format, chain HA [auth I]	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 FA [auth J] SDF format, chain FC [auth A] 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 VA [auth M] SDF format, chain XB [auth C] SDF format, chain ZA [auth L] SDF format, chain TB [auth D] SDF format, chain HB [auth G] SDF format, chain DB [auth K] SDF format, chain BC [auth B] MOL2 format, chain FA [auth J] MOL2 format, chain FC [auth A] 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 VA [auth M] MOL2 format, chain XB [auth C] MOL2 format, chain ZA [auth L] MOL2 format, chain TB [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain DB [auth K] MOL2 format, chain BC [auth B] mmCIF format, chain FA [auth J] mmCIF format, chain FC [auth A] 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 VA [auth M] mmCIF format, chain XB [auth C] mmCIF format, chain ZA [auth L] mmCIF format, chain TB [auth D] mmCIF format, chain HB [auth G] mmCIF format, chain DB [auth K] mmCIF format, chain BC [auth B]	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 GB [auth G] SDF format, chain KB [auth F] SDF format, chain OB [auth E] SDF format, chain QA [auth N] SDF format, chain UA [auth M] SDF format, chain WB [auth C] SDF format, chain YA [auth L] SDF format, chain SB [auth D] SDF format, chain MA [auth H] SDF format, chain IA [auth I] SDF format, chain EC [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain GB [auth G] MOL2 format, chain KB [auth F] MOL2 format, chain OB [auth E] MOL2 format, chain QA [auth N] MOL2 format, chain UA [auth M] MOL2 format, chain WB [auth C] MOL2 format, chain YA [auth L] MOL2 format, chain SB [auth D] MOL2 format, chain MA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain EC [auth A] mmCIF format, chain AC [auth B] mmCIF format, chain CB [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain GB [auth G] mmCIF format, chain KB [auth F] mmCIF format, chain OB [auth E] mmCIF format, chain QA [auth N] mmCIF format, chain UA [auth M] mmCIF format, chain WB [auth C] mmCIF format, chain YA [auth L] mmCIF format, chain SB [auth D] mmCIF format, chain MA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain EC [auth A]	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: 0.300 (DCC)
R-Value Work: 0.270 (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

View Full Validation Report

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