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- PDB-6siv: Structure of HPV16 E6 oncoprotein in complex with mutant IRF3 Lxx... -

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Basic information

Entry
Database: PDB / ID: 6siv
TitleStructure of HPV16 E6 oncoprotein in complex with mutant IRF3 LxxLL motif
Components
  • Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3
  • Protein E6
KeywordsVIRAL PROTEIN / HPV16 E6 protein / IRF3 mutant / LxxLL motif
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / symbiont-mediated perturbation of host apoptosis / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / regulation of proteolysis / IRF3-mediated induction of type I IFN ...symbiont-mediated suppression of host transcription / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / programmed necrotic cell death / symbiont-mediated perturbation of host apoptosis / TRIF-dependent toll-like receptor signaling pathway / signal transduction involved in regulation of gene expression / regulation of proteolysis / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / activation of GTPase activity / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / mRNA transcription / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / DNA-binding transcription activator activity / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / immune system process / cellular response to exogenous dsRNA / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / positive regulation of interferon-alpha production / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / positive regulation of type I interferon production / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / antiviral innate immune response / lipopolysaccharide-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interferon-beta production / Regulation of innate immune responses to cytosolic DNA / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / promoter-specific chromatin binding / Negative regulators of DDX58/IFIH1 signaling / PDZ domain binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Evasion by RSV of host interferon responses / DNA-binding transcription repressor activity, RNA polymerase II-specific / ISG15 antiviral mechanism / Interferon gamma signaling / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / TRAF3-dependent IRF activation pathway / outer membrane-bounded periplasmic space / regulation of inflammatory response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA-binding transcription activator activity, RNA polymerase II-specific / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / sequence-specific DNA binding / host cell cytoplasm / periplasmic space / DNA-binding transcription factor activity, RNA polymerase II-specific / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / innate immune response / virus-mediated perturbation of host defense response / DNA-templated transcription / DNA damage response / host cell nucleus / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
E6 early regulatory protein / CRO Repressor / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain ...E6 early regulatory protein / CRO Repressor / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltopentaose / Protein E6 / Maltose/maltodextrin-binding periplasmic protein / Interferon regulatory factor 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsSuarez, I.P. / Cousido-Siah, A. / Bonhoure, A. / Mitschler, A. / Podjarny, A. / Trave, G.
Funding support France, United States, 3items
OrganizationGrant numberCountry
French League Against Cancerequipe labellisee 2015 and fellowship AB France
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA134737 United States
Foundation for Medical Researchfellowship to IPS France
CitationJournal: To be published
Title: Deciphering the molecular and structural interaction between IRF3 and HPV16 E6
Authors: Poirson, J. / Suarez, I.P. / Cousido-Siah, A. / Forster, A. / Chebaro, Y. / Mitschler, A. / Straub, M. / Altschuh, D. / Podjarny, A. / Trave, G. / Masson, M.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3
B: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2035
Polymers60,2432
Non-polymers9603
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint13 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.031, 132.467, 42.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Interferon regulatory factor 3 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IRF-3


Mass: 41804.199 Da / Num. of mol.: 1
Mutation: K84A,K240A,E360A,K363A,D364A,N2146E,M2147E,V2148R,K84A,K240A,E360A,K363A,D364A,N2146E,M2147E,V2148R,K84A,K240A,E360A,K363A,D364A,N2146E,M2147E,V2148R,K84A,K240A,E360A,K363A,D364A,N2146E,M2147E,V2148R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, IRF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: Q14653
#2: Protein Protein E6


Mass: 18439.256 Da / Num. of mol.: 1 / Mutation: F1047R,C1080S,C1097S,C1111S,C1140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Gene: E6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03126
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: evaporation / Details: PEG 1500 30%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.752→48.516 Å / Num. obs: 104672 / % possible obs: 97.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.54
Reflection shellResolution: 1.752→1.86 Å / Num. unique obs: 16656 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
PHENIX1.16rc1_3531refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→48.516 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2202 --
Rwork0.1824 --
obs-54989 97.95 %
Refinement stepCycle: LAST / Resolution: 1.752→48.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 58 435 4587

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