8GB3

Structure of the Mycobacterium tuberculosis Hsp70 protein DnaK bound to the nucleotide exchange factor GrpE

• PDB DOI: https://doi.org/10.2210/pdb8GB3/pdb
• EM Map EMD-29912: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-24 Released: 2024-01-31 
• Deposition Author(s): Xiao, X., Li, H.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled

Xiao, X., Fay, A., Molina, P.S., Kovach, A., Glickman, M.S., Li, H.

(2024) Nat Commun 15: 660

• DOI: https://doi.org/10.1038/s41467-024-44933-9

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 116.03 kDa 
• Atom Count: 5,537 
• Modelled Residue Count: 735 
• Deposited Residue Count: 1,095 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A [auth D]	625	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dnaK_2, dnaK, E5M05_19850, ERS007703_00955, ERS023446_02581, ERS027651_01905, FCN16_12395, SAMEA2682864_01182, SAMEA2683035_02658
UniProt
Find proteins for A0A045JRR0 (Mycobacterium tuberculosis) Explore A0A045JRR0  Go to UniProtKB:  A0A045JRR0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein GrpE	B [auth E], C [auth F]	235	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: grpE, E5M05_19845, E5M52_19255, E5M78_19290, ERS007681_03281, ERS007703_00954, ERS024276_02384, SAMEA2683035_02659
UniProt
Find proteins for A0A045J399 (Mycobacterium tuberculosis) Explore A0A045J399  Go to UniProtKB:  A0A045J399

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Xiao, X., Li, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	R01

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Database references