6SJV | pdb_00006sjv

Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif

• PDB DOI: https://doi.org/10.2210/pdb6SJV/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli, human papillomavirus 18, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-08-14 Released: 2019-09-04 
• Deposition Author(s): Suarez, I.P., Cousido-Siah, A., Bonhoure, A., Kostmann, C., 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 

Literature

Cellular target recognition by HPV18 and HPV49 oncoproteins

Suarez, I.P., Bonhoure, A., Cousido-Siah, A., Chebaro, Y., Kostmann, C., Eberling, P., Altschuh, D., Mitschler, A., Podjarny, A., Trave, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.12 kDa 
• Atom Count: 4,307 
• Modeled Residue Count: 529 
• Deposited Residue Count: 543 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A	A	543	Escherichia coli, human papillomavirus 18, Homo sapiens This entity is chimeric	Mutation(s): 7  Gene Names: malE, EPS91_05465, NCTC8450_00456, NCTC9775_03059, E6, UBE3A, E6AP, EPVE6AP, HPVE6A EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for P06463 (Human papillomavirus type 18) Explore P06463  Go to UniProtKB:  P06463
Find proteins for Q05086 (Homo sapiens) Explore Q05086  Go to UniProtKB:  Q05086
PHAROS:  Q05086 GTEx:  ENSG00000114062
UniProt Groups	Q05086P06463

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.825	α = 90
b = 106.825	β = 90
c = 100.377	γ = 120

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., Kostmann, C., 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	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, Non-polymer description, Structure summary
• Version 2.1: 2022-03-30
  Changes: Author supporting evidence, Database references, Structure summary
• Version 2.2: 2024-06-19
  Changes: Data collection