4XC5

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.190
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.00433-15
Primary Citation of 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.

Organizational Affiliation

Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04506
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	G [auth A] H [auth A] L [auth B] M [auth B] N [auth B] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C]	F [auth A], K [auth B], Q [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C]	D [auth A], I [auth B], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C]	E [auth A], J [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.190
R-Value Observed: 0.193
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

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Entry History & Funding Information

Deposition Data

Released Date: 2015-04-01

Deposition Author(s):

Reiss, K.

Stehle, T.

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

Revision History (Full details and data files)

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

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