7TFM

Atomic Structure of the Leishmania spp. Hsp100 N-Domain

• PDB DOI: https://doi.org/10.2210/pdb7TFM/pdb

• Classification: CHAPERONE
• Organism(s): Leishmania mexicana MHOM/GT/2001/U1103
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-01-06 Released: 2022-02-16 
• Deposition Author(s): Mercado, J.M., Lee, S., Chang, C., Sung, N., Soong, L., Catic, A., Tsai, F.T.F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 

Literature

Atomic structure of the Leishmania spp. Hsp100 N-domain.

Mercado, J.M., Lee, S., Chang, C., Sung, N., Soong, L., Catic, A., Tsai, F.T.F.

(2022) Proteins 90: 1242-1246

• PubMed: 35122310 
• DOI: https://doi.org/10.1002/prot.26310
• Primary Citation of Related Structures:  
  7TFM


• PubMed Abstract: 
  

  Hsp100 is an ATP-dependent unfoldase that promotes protein disaggregation or facilitates the unfolding of aggregation-prone polypeptides marked for degradation. Recently, new Hsp100 functions are emerging. In Plasmodium, an Hsp100 drives malaria protein export, presenting a novel drug target. Whether Hsp100 has a similar function in other protists is unknown. We present the 1.06 Å resolution crystal structure of the Hsp100 N-domain from Leishmania spp., the causative agent of leishmaniasis in humans. Our structure reveals a network of methionines and aromatic amino acids that define the putative substrate-binding site and likely evolved to protect Hsp100 from oxidative damage in host immune cells.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.52 kDa 
• Atom Count: 1,349 
• Modelled Residue Count: 142 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease subunit, heat shock protein 100 (HSP100)	A	158	Leishmania mexicana MHOM/GT/2001/U1103	Mutation(s): 0  Gene Names: LMXM_08_29_1270
UniProt
Find proteins for E9ALU6 (Leishmania mexicana (strain MHOM/GT/2001/U1103)) Explore E9ALU6  Go to UniProtKB:  E9ALU6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.971	α = 90
b = 60.971	β = 90
c = 71.807	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Mercado, J.M., Lee, S., Chang, C., Sung, N., Soong, L., Catic, A., Tsai, F.T.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM104980
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM142143
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK115454
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR140038
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10-OD030246
Welch Foundation	United States	Q-1530-20190330
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008289

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2022-04-27
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description