4GJT

complex structure of nectin-4 bound to MV-H

• PDB DOI: https://doi.org/10.2210/pdb4GJT/pdb

• Classification: MEMBRANE PROTEIN/VIRAL PROTEIN
• Organism(s): Measles virus strain Ichinose-B95a, Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-10 Released: 2012-10-10 
• Deposition Author(s): Zhang, X., Lu, G., Qi, J., Li, Y., He, Y., Xu, X., Shi, J., Zhang, C., Yan, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.260 
• R-Value Observed: 0.261 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.87 kDa 
• Atom Count: 5,020 
• Modelled Residue Count: 637 
• Deposited Residue Count: 719 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin glycoprotein	A	473	Measles virus strain Ichinose-B95a	Mutation(s): 0  Gene Names: H, hemagglutinin
UniProt
Find proteins for Q786F2 (Measles virus (strain Ichinose-B95a)) Explore Q786F2  Go to UniProtKB:  Q786F2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 4	B, C	123	Homo sapiens	Mutation(s): 0  Gene Names: LNIR, nectin-4, PRR4, PVRL4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY8 (Homo sapiens) Explore Q96NY8  Go to UniProtKB:  Q96NY8
PHAROS:  Q96NY8 GTEx:  ENSG00000143217

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.260 
• R-Value Observed: 0.261 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.35	α = 90
b = 171.778	β = 90
c = 117.44	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Zhang, X., Lu, G., Qi, J., Li, Y., He, Y., Xu, X., Shi, J., Zhang, C., Yan, J., Gao, G.F.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary