6SJA

Structure of HPV16 E6 oncoprotein in complex with IRF3 LxxLL motif

• PDB DOI: https://doi.org/10.2210/pdb6SJA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, Human papillomavirus 16
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-13 Released: 2019-09-04 
• Deposition Author(s): Suarez, I.P., Cousido-Siah, A., Bonhoure, A., Mitschler, A., Podjarny, A., Trave, G.
• Funding Organization(s): French League Against Cancer, National Institutes of Health/National Cancer Institute (NIH/NCI), Foundation for Medical Research (France)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Deciphering de molecular and structural interaction between IRF3 and HPV16 E6

Poirson, J., Suarez, I.P., Cousido-Siah, A., Forster, A., Chebaro, Y., Mitschler, A., Straub, M., Altschuh, D., Podjarny, A., Trave, G., Masson, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 61.13 kDa 
• Atom Count: 4,668 
• Modelled Residue Count: 517 
• Deposited Residue Count: 536 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3	A	383	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: malE, b4034, JW3994, IRF3
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q14653 (Homo sapiens) Explore Q14653  Go to UniProtKB:  Q14653
PHAROS:  Q14653 GTEx:  ENSG00000126456
UniProt Groups	Q14653P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E6	B	153	Human papillomavirus 16	Mutation(s): 5  Gene Names: E6
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126  Go to UniProtKB:  P03126

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	5		N/A
Glycosylation Resources
GlyTouCan:  G50146AM GlyCosmos:  G50146AM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.659	α = 90
b = 132.87	β = 90
c = 43.025	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: 2019-09-04 
Deposition Author(s): Suarez, I.P., Cousido-Siah, A., Bonhoure, A., Mitschler, A., Podjarny, A., Trave, G.

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Funding Organization	Location	Grant Number
French League Against Cancer	France	equipe labellisee 2015 and fellowship AB
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA134737
Foundation for Medical Research (France)	France	fellowship to IPS

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Derived calculations, Structure summary
• Version 3.0: 2022-07-20
  Type: Coordinate replacement
  Reason: Missing anisotropic B-factor
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary
• Version 3.1: 2024-01-24
  Changes: Data collection, Refinement description