5T1D

Crystal structure of EBV gHgL/gp42/E1D1 complex

• PDB DOI: https://doi.org/10.2210/pdb5T1D/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human herpesvirus 4 strain B95-8, human gammaherpesvirus 4, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-08-18 Released: 2016-12-28 
• Deposition Author(s): Sathiyamoorthy, K., Jardetzky, T.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 154.38 kDa 
• Atom Count: 10,617 
• Modelled Residue Count: 1,356 
• Deposited Residue Count: 1,388 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A	655	Human herpesvirus 4 strain B95-8	Mutation(s): 0  Gene Names: gH, BXLF2
UniProt
Find proteins for P03231 (Epstein-Barr virus (strain B95-8)) Explore P03231  Go to UniProtKB:  P03231

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B	112	Human herpesvirus 4 strain B95-8	Mutation(s): 0  Gene Names: gL, BKRF2
UniProt
Find proteins for P03212 (Epstein-Barr virus (strain B95-8)) Explore P03212  Go to UniProtKB:  P03212

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 42	C	191	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BZLF2
UniProt
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1)) Explore P0C6Z5  Go to UniProtKB:  P0C6Z5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
E1D1 IgG2a heavy chain	D [auth H]	213	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
E1D1 IgG2a light chain	E [auth L]	217	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], G [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.51	α = 90
b = 166	β = 90
c = 272.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Sathiyamoorthy, K., Jardetzky, T.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI119480
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI076183
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA117794

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2017-01-04
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary