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- PDB-6sja: Structure of HPV16 E6 oncoprotein in complex with IRF3 LxxLL motif -

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Basic information

Entry
Database: PDB / ID: 6sja
TitleStructure of HPV16 E6 oncoprotein in complex with 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 suppression of host apoptosis / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / 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 suppression of host apoptosis / TRIF-dependent toll-like receptor signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / regulation of Cdc42 protein signal transduction / mRNA transcription / signal transduction involved in regulation of gene expression / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / DNA-binding transcription activator activity / cellular response to exogenous dsRNA / detection of maltose stimulus / maltose transport complex / carbohydrate transport / positive regulation of interferon-alpha production / regulation of proteolysis / carbohydrate transmembrane transporter activity / immune system process / maltose binding / positive regulation of type I interferon production / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / antiviral innate immune response / TICAM1-dependent activation of IRF3/IRF7 / ATP-binding cassette (ABC) transporter complex / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / cell chemotaxis / PDZ domain binding / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / cellular response to virus / ISG15 antiviral mechanism / DNA-binding transcription repressor activity, RNA polymerase II-specific / Interferon gamma signaling / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / outer membrane-bounded periplasmic space / regulation of inflammatory response / TRAF3-dependent IRF activation pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / defense response to virus / sequence-specific DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / DNA-binding transcription factor activity, RNA polymerase II-specific / periplasmic space / positive regulation of canonical NF-kappaB signal transduction / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / innate immune response / apoptotic process / DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 1.5 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 Research (France)fellowship to IPS France
CitationJournal: To be published
Title: Deciphering de 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 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 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 2.1Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / pdbx_audit_support / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct_conn / symmetry
Item: _cell.volume / _entity.pdbx_mutation ..._cell.volume / _entity.pdbx_mutation / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_number_measured_all / _reflns.pdbx_redundancy / _software.version / _struct_conn.pdbx_dist_value / _symmetry.space_group_name_Hall
Description: Missing anisotropic B-factor / Provider: author / Type: Coordinate replacement
Revision 3.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,1325
Polymers60,1722
Non-polymers9603
Water8,665481
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.659, 132.870, 43.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: 41733.203 Da / Num. of mol.: 1 / Mutation: E360A,K363A,D364A,K84A,K240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, IRF3 / Production host: Escherichia coli (E. coli) / 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 (E. coli) / 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 / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.8 / 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: 1.5→45.832 Å / Num. obs: 170435 / % possible obs: 98.1 % / Redundancy: 6.999 % / Biso Wilson estimate: 27.053 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Χ2: 1.062 / Net I/σ(I): 15.95 / Num. measured all: 1192946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.596.7041.151.6518066628150269480.6181.24795.7
1.59-1.77.2990.7042.8618759326350257010.8530.75797.5
1.7-1.837.2070.3914.9817373624600241050.9430.42198
1.83-2.016.9230.2088.8815374322599222070.9820.22598.3
2.01-2.256.570.1115.6313287920487202240.9940.1298.7
2.25-2.597.3830.07324.8913196518046178750.9970.07899.1
2.59-3.177.1640.04935.810838315243151290.9990.05399.3
3.17-4.486.3510.03349.347450711791117320.9990.03699.5
4.48-45.8327.5950.02661.5849474655065140.9990.02899.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIZ

4giz


Resolution: 1.5→45.83 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 8529 5.01 %
Rwork0.159 161863 -
obs0.1606 170392 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.38 Å2 / Biso mean: 29.1974 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 1.5→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 58 486 4619
Biso mean--28.88 37.54 -
Num. residues----517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.32392550.29564922517790
1.52-1.530.2672890.26195404569397
1.53-1.550.3082820.24815317559997
1.55-1.570.23292810.23285330561197
1.57-1.590.25382860.2195405569197
1.59-1.610.25292810.21285309559097
1.61-1.640.22532870.20865337562497
1.64-1.660.25142860.20095421570798
1.66-1.690.2292800.195333561398
1.69-1.720.19662880.17345411569998
1.72-1.740.19552820.17165342562498
1.74-1.780.20872820.16855434571698
1.78-1.810.21482810.15875355563698
1.81-1.850.22012820.15645399568198
1.85-1.890.18362890.14955425571498
1.89-1.930.19832850.1465376566198
1.93-1.980.18262920.15065432572498
1.98-2.030.19962850.14785431571699
2.03-2.090.18312800.14865401568199
2.09-2.160.16952840.14185474575899
2.16-2.240.17122900.14285425571599
2.24-2.330.17312860.13995446573299
2.33-2.430.17612890.14615443573299
2.43-2.560.19472900.14835436572699
2.56-2.720.21132850.15775454573999
2.72-2.930.19982880.15885466575499
2.93-3.230.19632850.16865479576499
3.23-3.70.2032860.15545480576699
3.7-4.650.14632860.137154935779100
4.66-45.830.16972870.161154835770100

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