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- PDB-6sjv: Structure of HPV18 E6 oncoprotein in complex with mutant E6AP Lxx... -

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Basic information

Entry
Database: PDB / ID: 6sjv
TitleStructure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif
ComponentsMaltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A
KeywordsVIRAL PROTEIN / HPV18 E6 protein / E6AP / LxxLL motif
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior ...sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior / carbohydrate transmembrane transporter activity / protein autoubiquitination / protein K48-linked ubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / response to cocaine / positive regulation of protein ubiquitination / PDZ domain binding / response to progesterone / regulation of synaptic plasticity / response to hydrogen peroxide / regulation of circadian rhythm / brain development / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / outer membrane-bounded periplasmic space / ubiquitin-dependent protein catabolic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / negative regulation of DNA-templated transcription / DNA-templated transcription / glutamatergic synapse / host cell nucleus / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / HECT domain / HECT, E3 ligase catalytic domain ...Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / 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
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Protein E6 / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human papillomavirus type 18
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.029 Å
AuthorsSuarez, I.P. / Cousido-Siah, A. / Bonhoure, A. / Kostmann, C. / 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: Cellular target recognition by HPV18 and HPV49 oncoproteins
Authors: Suarez, I.P. / Bonhoure, A. / Cousido-Siah, A. / Chebaro, Y. / Kostmann, C. / Eberling, P. / Altschuh, D. / Mitschler, A. / Podjarny, A. / Trave, G.
History
DepositionAug 14, 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 / Non-polymer description / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
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
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: Maltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1254
Polymers60,6521
Non-polymers4733
Water2,180121
1
A: Maltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A
hetero molecules

A: Maltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2508
Polymers121,3042
Non-polymers9466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Unit cell
Length a, b, c (Å)106.825, 106.825, 100.377
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-2621-

HOH

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Components

#1: Protein Maltodextrin-binding protein,Protein E6,Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 60651.824 Da / Num. of mol.: 1
Mutation: K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R
Source method: isolated from a genetically manipulated source
Details: Chain A, res 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot: P0AEX9. Natural source organism: Escherichia coli. Chain A, res 1001-1143: HPV18 E6 Protein, Uniprot: P06463. Natural source ...Details: Chain A, res 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot: P0AEX9. Natural source organism: Escherichia coli. Chain A, res 1001-1143: HPV18 E6 Protein, Uniprot: P06463. Natural source organism: Human papilloma virus type 18. Chain A, residues 2380-2394: E6AP, Uniprot: Q05086. Natural source organis: Homo sapiens.,Chain A, res 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot: P0AEX9. Natural source organism: Escherichia coli. Chain A, res 1001-1143: HPV18 E6 Protein, Uniprot: P06463. Natural source organism: Human papilloma virus type 18. Chain A, residues 2380-2394: E6AP, Uniprot: Q05086. Natural source organis: Homo sapiens.,Chain A, res 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot: P0AEX9. Natural source organism: Escherichia coli. Chain A, res 1001-1143: HPV18 E6 Protein, Uniprot: P06463. Natural source organism: Human papilloma virus type 18. Chain A, residues 2380-2394: E6AP, Uniprot: Q05086. Natural source organis: Homo sapiens.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Human papillomavirus type 18, (gene. exp.) Homo sapiens (human)
Gene: malE, EPS91_05465, NCTC8450_00456, NCTC9775_03059, E6, UBE3A, E6AP, EPVE6AP, HPVE6A
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A376KDN7, UniProt: P06463, UniProt: Q05086, HECT-type E3 ubiquitin transferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: Sodium Cacodylate 100 mM pH 6.5, PEG 8000 5%, 2-methyl-2,4-pentanediol 40%

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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: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.029→19.792 Å / Num. obs: 82043 / % possible obs: 98.9 % / Redundancy: 9.8 % / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 2.0293→2.1017 Å / Num. unique obs: 42645 / CC1/2: 0.563

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.029→19.792 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2424 --
Rwork0.2032 --
obs-42645 98.83 %
Refinement stepCycle: LAST / Resolution: 2.029→19.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4157 0 25 121 4303

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