6SIV | pdb_00006siv

Structure of HPV16 E6 oncoprotein in complex with mutant IRF3 LxxLL motif

PDB DOI: https://doi.org/10.2210/pdb6SIV/pdb

Classification: VIRAL PROTEIN
Organism(s): Escherichia coli K-12, Homo sapiens, Human papillomavirus 16
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-08-12 Released: 2019-08-21
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Deciphering the 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.

Macromolecule Content

Total Structure Weight: 61.2 kDa
Atom Count: 4,614
Modeled Residue Count: 519
Deposited Residue Count: 536
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3	A	383	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 6 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q14653P0AEX9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03126
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G50146AM GlyCosmos: G50146AM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900030 Query on PRD_900030	C	alpha-maltopentaose	Oligosaccharide / Substrate analog		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.180 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.031	α = 90
b = 132.467	β = 90
c = 42.634	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2019-08-21
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: 2022-03-30
Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
Version 2.2: 2024-06-19
Changes: Data collection