5I72

Crystal structure of the oligomeric form of the Lassa virus matrix protein Z

• PDB DOI: https://doi.org/10.2210/pdb5I72/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Lassa virus Josiah
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-16 Released: 2016-03-09 
• Deposition Author(s): Hastie, K., Zandonatti, M., Liu, T., Li, S., Woods Jr, V., Saphire, E.O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.

Hastie, K.M., Zandonatti, M., Liu, T., Li, S., Woods, V.L., Saphire, E.O.

(2016) J Virol 90: 4556-4562

• PubMed: 26912609 
• DOI: https://doi.org/10.1128/JVI.02896-15
• Primary Citation of Related Structures:  
  5I72


• PubMed Abstract: 
  

  The arenavirus matrix protein Z is highly multifunctional and occurs in both monomeric and oligomeric forms. The crystal structure of a dodecamer of Z from Lassa virus, presented here, illustrates a ring-like structure with a highly basic center. Mutagenesis demonstrates that the dimeric interface within the dodecamer and a Lys-Trp-Lys triad at the center of the ring are important for oligomerization. This structure provides an additional template to explore the many functions of Z.

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Organizational Affiliation: 

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.43 kDa 
• Atom Count: 826 
• Modelled Residue Count: 104 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein Z	A, B	53	Lassa virus Josiah	Mutation(s): 0
UniProt
Find proteins for O73557 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore O73557  Go to UniProtKB:  O73557

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.209 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.961	α = 90
b = 116.961	β = 90
c = 82.544	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Hastie, K., Zandonatti, M., Liu, T., Li, S., Woods Jr, V., Saphire, E.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI2008031

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2022-03-23
  Changes: Author supporting evidence, Database references