5NET

Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A.

• PDB DOI: https://doi.org/10.2210/pdb5NET/pdb
• EM Map EMD-3634: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Foot-and-mouth disease virus, Homo sapiens
• Expression System: Cricetinae gen. sp., Homo sapiens
• Mutation(s): No 


• Deposited: 2017-03-11 Released: 2017-06-21 
• Deposition Author(s): Kotecha, A., Stuart, D.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

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

Macromolecule Content

• Total Structure Weight: 201.25 kDa 
• Atom Count: 13,559 
• Modelled Residue Count: 1,717 
• Deposited Residue Count: 1,795 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O1 Manisa VP1	A [auth 1]	208	Foot-and-mouth disease virus	Mutation(s): 0
UniProt
Find proteins for Q6PMW3 (Foot-and-mouth disease virus O) Explore Q6PMW3  Go to UniProtKB:  Q6PMW3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O1 Manisa VP2	B [auth 2]	218	Foot-and-mouth disease virus	Mutation(s): 0
UniProt
Find proteins for D1H101 (Foot-and-mouth disease virus) Explore D1H101  Go to UniProtKB:  D1H101

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
O1 Manisa VP3	C [auth 3]	220	Foot-and-mouth disease virus	Mutation(s): 0
UniProt
Find proteins for Q6PMW3 (Foot-and-mouth disease virus O) Explore Q6PMW3  Go to UniProtKB:  Q6PMW3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
O1 Manisa VP4	D [auth 4]	85	Foot-and-mouth disease virus	Mutation(s): 0
UniProt
Find proteins for D1H101 (Foot-and-mouth disease virus) Explore D1H101  Go to UniProtKB:  D1H101

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	E [auth A]	594	Homo sapiens	Mutation(s): 0  Gene Names: ITGAV, MSK8, VNRA
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756  Go to UniProtKB:  P06756
PHAROS:  P06756 GTEx:  ENSG00000138448

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-6	F [auth B]	470	Homo sapiens	Mutation(s): 0  Gene Names: ITGB6
UniProt & NIH Common Fund Data Resources
Find proteins for P18564 (Homo sapiens) Explore P18564  Go to UniProtKB:  P18564
PHAROS:  P18564 GTEx:  ENSG00000115221

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], H [auth D]	3		N/A
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	I [auth E]	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth G]	4		N/A
Glycosylation Resources
GlyTouCan:  G81874LD GlyCosmos:  G81874LD GlyGen:  G81874LD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	O [auth A], T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	L [auth 3], M [auth 3], N [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA	P [auth A], Q [auth A], R [auth A], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	I [auth E]	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	1.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Kotecha, A., Stuart, D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G1000099
Medical Research Council (United Kingdom)	United Kingdom	G1100525/1
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence, Data collection, Experimental preparation, Refinement description
• Version 1.2: 2017-10-04
  Changes: Structure summary
• Version 1.3: 2018-03-28
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary