4ODB | pdb_00004odb

Crystal structure of the T1L reovirus attachment protein sigma1 in complex with Junctional Adhesion Molecule-A

• PDB DOI: https://doi.org/10.2210/pdb4ODB/pdb

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


• Deposited: 2014-01-10 Released: 2015-04-01 
• Deposition Author(s): Stettner, E., Stehle, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.242 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The JAM-A binding site is conserved in reovirus sigma1: Structure of the T1L sigma1-JAM-A complex

Stettner, E., Reiss, K., Dietrich, M., Stehle, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content 

• Total Structure Weight: 90.93 kDa 
• Atom Count: 6,276 
• Modeled Residue Count: 792 
• Deposited Residue Count: 807 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein sigma-1	A, B, C	165	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Junctional adhesion molecule A	D, E, F	104	Homo sapiens	Mutation(s): 0  Gene Names: F11R, JAM1, JCAM, UNQ264/PRO301
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y624 (Homo sapiens) Explore Q9Y624  Go to UniProtKB:  Q9Y624
PHAROS:  Q9Y624 GTEx:  ENSG00000158769

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.242 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.77	α = 90
b = 156.77	β = 90
c = 96.54	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary