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- PDB-6slm: Crystal structure of full-length HPV31 E6 oncoprotein in complex ... -

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Basic information

Entry
Database: PDB / ID: 6slm
TitleCrystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of ubiquitin ligase E6AP
ComponentsMaltose/maltodextrin-binding periplasmic protein,Protein E6,Ubiquitin-protein ligase E3A
KeywordsONCOPROTEIN / viral protein
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 / detection of maltose stimulus ...: / : / 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 / detection of maltose stimulus / maltose transport complex / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / protein autoubiquitination / protein K48-linked ubiquitination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / ATP-binding cassette (ABC) transporter complex / proteasome complex / cell chemotaxis / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / periplasmic space / 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 / DNA-templated transcription / glutamatergic synapse / DNA damage response / host cell nucleus / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / membrane / 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 / Maltose/maltodextrin-binding periplasmic protein / Protein E6 / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human papillomavirus type 31
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsConrady, M. / Gogl, G. / Cousido-Siah, A. / Mitschler, A. / Trave, G. / Simon, C.
Funding support France, 1items
OrganizationGrant numberCountry
French League Against Cancerequipe labellisee 2015 France
CitationJournal: J.Virol. / Year: 2020
Title: Structure of High-Risk Papillomavirus 31 E6 Oncogenic Protein and Characterization of E6/E6AP/p53 Complex Formation.
Authors: Conrady, M.C. / Suarez, I. / Gogl, G. / Frecot, D.I. / Bonhoure, A. / Kostmann, C. / Cousido-Siah, A. / Mitschler, A. / Lim, J. / Masson, M. / Iftner, T. / Stubenrauch, F. / Trave, G. / Simon, C.
History
DepositionAug 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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,Protein E6,Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6236
Polymers60,9661
Non-polymers6575
Water55831
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint3 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.640, 113.640, 185.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1076-

PHE

21A-1076-

PHE

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Protein E6,Ubiquitin-protein ligase E3A / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / E6AP ubiquitin-protein ligase ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / 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: 60966.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Human papillomavirus type 31, (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, E6, UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: P17386, 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM tri-lithium citrate, 20% PEG 33350 protein concentration: 30mg/ml cryo condition: 35% glycerol

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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: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.25 Å / Num. obs: 18049 / % possible obs: 99.1 % / Redundancy: 19.4 % / Biso Wilson estimate: 62.24 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.23 / Net I/σ(I): 14.49
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 18.9 % / Mean I/σ(I) obs: 1.57 / Num. unique obs: 1295 / CC1/2: 0.52 / Rrim(I) all: 2.076

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XR8

4xr8


Resolution: 2.8→49.21 Å / SU ML: 0.3943 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6874
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 894 4.95 %Random selection
Rwork0.23 ---
obs0.2319 18043 99.37 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 85.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 37 31 4270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344347
X-RAY DIFFRACTIONf_angle_d0.6195898
X-RAY DIFFRACTIONf_chiral_restr0.0438648
X-RAY DIFFRACTIONf_plane_restr0.0033758
X-RAY DIFFRACTIONf_dihedral_angle_d16.92011596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.34241290.31572791X-RAY DIFFRACTION98.95
2.98-3.210.37041530.30722770X-RAY DIFFRACTION98.98
3.21-3.530.30071490.25982806X-RAY DIFFRACTION99.36
3.53-4.040.28251540.23062827X-RAY DIFFRACTION99.4
4.04-5.090.2211500.19542874X-RAY DIFFRACTION99.7
5.09-49.2080.24541590.20733081X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26320798294-0.6313944678650.2030204631954.78291781951-2.008597111322.955301865110.0510272464139-0.1535714942480.0508642453094-0.448526821170.7404604916931.112807524090.0648645992414-0.931369472099-0.5225605978260.505583362619-0.150732458228-0.2027432651690.7514881662520.400761126390.88754408917-17.170738202-48.13152139154.09642888719
24.72384806322-1.838720270262.345552846683.891906236-2.595037654846.42571461851-0.3153386160930.164453803174-0.05956234176830.02627262570950.01019700129-0.179813250819-0.1854846945510.0245994872830.2886775835280.29708139686-0.07625324616330.07312876660920.3252072626-0.0380721501110.2792758882274.2831021776-20.7409507815-15.4806485212
35.71057592681-2.77250493828-1.768183274496.32331245254-0.6958836830039.02751599020.1049337344930.169362529991-0.100289868944-0.0387496054712-0.482321335128-0.7048650827430.02167661186390.295435249420.3213587694610.389537810482-0.0990294825501-0.04019421316270.5497290894760.04048173272210.5338626255510.0260139809-21.6193834766-21.0675862547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 631 through 1011 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1012 through 1138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1139 through 1179 )

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