7KLU | pdb_00007klu

Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb7KLU/pdb
EM Map EMD-22918: EMDB EMDataResource

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

Deposited: 2020-11-01 Released: 2021-11-03
Deposition Author(s): Liu, Y.X., Agard, D.A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM analysis of human mitochondrial Hsp90 in multiple tetrameric states

Liu, Y.X., Agard, D.A., Elnatan, D., Sun, M., Larson, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 362.71 kDa
Atom Count: 19,742
Modelled Residue Count: 2,452
Deposited Residue Count: 3,206
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 75 kDa, mitochondrial, SpyCatcher	A, C [auth D]	774	Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 0 Gene Names: TRAP1, HSP75
UniProt & NIH Common Fund Data Resources
Find proteins for Q12931 (Homo sapiens) Explore Q12931 Go to UniProtKB: Q12931
PHAROS: Q12931 GTEx: ENSG00000126602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12931
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)	B, D [auth C]	829	Homo sapiens, synthetic construct	Mutation(s): 0 Gene Names: TRAP1, HSP75, SDHB, SDH, SDH1 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21912 (Homo sapiens) Explore P21912 Go to UniProtKB: P21912
PHAROS: P21912 GTEx: ENSG00000117118
Find proteins for Q12931 (Homo sapiens) Explore Q12931 Go to UniProtKB: Q12931
PHAROS: Q12931 GTEx: ENSG00000126602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P21912Q12931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain N [auth C]	E [auth A], H [auth B], K [auth D], N [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain N [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth D] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C]	G [auth A], J [auth B], M [auth D], P [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain P [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth D] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] mmCIF format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D]	F [auth A], I [auth B], L [auth D], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Liu, Y.X.

Agard, D.A.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
American Heart Association	United States	18POST33990362
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118099
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	U54CA209891
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	U01MH115747
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI135990