7TFM | pdb_00007tfm

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 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

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 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.
Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, Texas, USA.
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Department of Microbiology and Immunology, Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA.
Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular Virology and Microbiology, 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 
• Modeled 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 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

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