4XC5 | pdb_00004xc5

CRYSTAL STRUCTURE OF THE T1L REOVIRUS ATTACHMENT PROTEIN SIGMA1

• PDB DOI: https://doi.org/10.2210/pdb4XC5/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Mammalian orthoreovirus 1 Lang
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-17 Released: 2015-04-01 
• Deposition Author(s): Reiss, K., Stehle, T.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.223 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structure of Serotype 1 Reovirus Attachment Protein sigma 1 in Complex with Junctional Adhesion Molecule A Reveals a Conserved Serotype-Independent Binding Epitope.

Stettner, E., Dietrich, M.H., Reiss, K., Dermody, T.S., Stehle, T.

(2015) J Virol 89: 6136-6140

• PubMed: 25810543 
• DOI: https://doi.org/10.1128/JVI.00433-15
• Primary Citation Related Structures: 
  4XC5


• PubMed Abstract: 
  

  Mammalian orthoreoviruses use glycans and junctional adhesion molecule A (JAM-A) as attachment receptors. We determined the structure of serotype 1 reovirus attachment protein σ1 alone and in complex with JAM-A. Comparison with the structure of serotype 3 reovirus σ1 bound to JAM-A reveals that both σ1 proteins engage JAM-A with similar affinities and via conserved binding epitopes. Thus, σ1-JAM-A interactions are unlikely to explain the differences in pathogenesis displayed by these reovirus serotypes.

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Organizational Affiliation: 
• Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, Tennessee, USA Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA [e-mail] [e-mail].
Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 74.94 kDa 
• Atom Count: 3,951 
• Modeled Residue Count: 485 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein sigma-1	A, B, C	218	Mammalian orthoreovirus 1 Lang	Mutation(s): 0  Gene Names: S1
UniProt
Find proteins for P04506 (Reovirus type 1 (strain Lang)) Explore P04506  Go to UniProtKB:  P04506

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A], K [auth B], Q [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], I [auth B], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], J [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.223 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.93	α = 90
b = 112.96	β = 90
c = 113.22	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Reiss, K., Stehle, T.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	R01 AI076983

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Database references
• Version 1.2: 2015-05-13
  Changes: Database references
• Version 1.3: 2016-07-13
  Changes: Data collection
• Version 2.0: 2024-01-10
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description