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 
- 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)
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 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein H | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03231 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein L | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03212 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glycoprotein 42 | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0C6Z5 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
E1D1 IgG2a heavy chain | D [auth H] | 213 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
E1D1 IgG2a light chain | E [auth L] | 217 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
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 Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-12-28  Deposition Author(s): Sathiyamoorthy, K., Jardetzky, T.S.
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 (Full details and data files)
- 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