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- PDB-6smv: Structure of HPV49 E6 protein in complex with MAML1 LxxLL motif -

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Entry
Database: PDB / ID: 6smv
TitleStructure of HPV49 E6 protein in complex with MAML1 LxxLL motif
ComponentsMaltose/maltodextrin-binding periplasmic protein,Protein E6,Mastermind-like protein 1
KeywordsVIRAL PROTEIN / HPV49 E6 protein / MAML1 / LxxLL motif
Function / homology
Function and homology information


atrioventricular node cell development / MAML1-RBP-Jkappa- ICN1 complex / atrioventricular node development / positive regulation of transcription of Notch receptor target / NOTCH2 intracellular domain regulates transcription / symbiont-mediated perturbation of host apoptosis / myoblast differentiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription ...atrioventricular node cell development / MAML1-RBP-Jkappa- ICN1 complex / atrioventricular node development / positive regulation of transcription of Notch receptor target / NOTCH2 intracellular domain regulates transcription / symbiont-mediated perturbation of host apoptosis / myoblast differentiation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of myotube differentiation / detection of maltose stimulus / Notch-HLH transcription pathway / maltose transport complex / Formation of paraxial mesoderm / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Notch signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / peptide antigen binding / outer membrane-bounded periplasmic space / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / transcription coactivator activity / periplasmic space / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / nuclear speck / protein phosphorylation / virus-mediated perturbation of host defense response / DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / host cell nucleus / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / metal ion binding
Similarity search - Function
Neurogenic mastermind-like, N-terminal / Mastermind-like 1-3 / Neurogenic mastermind-like, N-terminal domain superfamily / : / : / MamL-1 domain / Mastermind-like 1/3, transactivation domain 2 / Mastermind-like 1/3, transactivation domain 1 / MamL-1 domain / E6 early regulatory protein ...Neurogenic mastermind-like, N-terminal / Mastermind-like 1-3 / Neurogenic mastermind-like, N-terminal domain superfamily / : / : / MamL-1 domain / Mastermind-like 1/3, transactivation domain 2 / Mastermind-like 1/3, transactivation domain 1 / MamL-1 domain / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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-maltotetraose / DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein / Protein E6 / Mastermind-like protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human papillomavirus type 49
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 Research (France)fellowship 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 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / chem_comp / entity / entity_src_gen / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][3] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][3] / _cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.gene_src_strain / _pdbx_audit_support.funding_organization / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.overall_SU_ML / _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_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _software.version / _struct_sheet.number_strands
Description: Polymer backbone linkage / Details: MBP density is poor and model was improved. / Provider: author / Type: Coordinate replacement
Revision 3.0Jul 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.pdbx_formal_charge / _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 3.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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,Mastermind-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1685
Polymers59,2641
Non-polymers9044
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 44.539, 94.237
Angle α, β, γ (deg.)90.000, 99.705, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Protein E6,Mastermind-like protein 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Mam-1


Mass: 59264.289 Da / Num. of mol.: 1 / Mutation: K84A,K240A,E360A,K363A,D364A,C1008A
Source method: isolated from a genetically manipulated source
Details: Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma ...Details: Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.,Residues 1-362: MALTOSE-BINDING PERIPLASMIC PROTEIN, Uniprot P0AEX9, Natural source: Escherichi coli. Residues 1001-1136: HPV49 E6 Protein, Uniprot P36813, Natural source: Human papilloma virus type 49. Residues 2002-2015: MAML1, Uniprot Q92585, Natural source: Homo sapiens.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Human papillomavirus type 49, (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, E6, MAML1, KIAA0200 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P36813, UniProt: Q92585
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][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: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.8 / Details: Lithium Acetate 200mM, PEG 3350 22.5%

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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: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→46.44 Å / Num. obs: 63547 / % possible obs: 97.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.93 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.14
Reflection shellResolution: 2.1439→2.2205 Å / Num. unique obs: 10215 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3769refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIZ

4giz


Resolution: 2.14→46.44 Å / SU ML: 0.3268 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 28.1416
RfactorNum. reflection% reflection
Rfree0.2553 3194 5.03 %
Rwork0.2178 --
obs0.2197 63536 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.08 Å2
Refinement stepCycle: LAST / Resolution: 2.14→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 54 171 4284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164227
X-RAY DIFFRACTIONf_angle_d0.43485749
X-RAY DIFFRACTIONf_chiral_restr0.0387642
X-RAY DIFFRACTIONf_plane_restr0.003735
X-RAY DIFFRACTIONf_dihedral_angle_d18.3961500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.180.35291400.32672570X-RAY DIFFRACTION96.99
2.18-2.210.31311340.31032595X-RAY DIFFRACTION95.86
2.21-2.250.29411390.32362584X-RAY DIFFRACTION96.56
2.25-2.280.38231400.34382597X-RAY DIFFRACTION98.56
2.28-2.330.37211400.28712661X-RAY DIFFRACTION96.62
2.33-2.370.361330.30242570X-RAY DIFFRACTION97.62
2.37-2.420.27711440.26352675X-RAY DIFFRACTION99.61
2.42-2.470.31721410.26412660X-RAY DIFFRACTION96.65
2.47-2.530.33821360.25742616X-RAY DIFFRACTION99.64
2.53-2.590.32251450.24132657X-RAY DIFFRACTION99.22
2.59-2.660.261370.24322613X-RAY DIFFRACTION97.55
2.66-2.740.27051420.232675X-RAY DIFFRACTION99.54
2.74-2.830.29041400.22132659X-RAY DIFFRACTION98.11
2.83-2.930.16861440.22842664X-RAY DIFFRACTION99.33
2.93-3.050.28151390.21722624X-RAY DIFFRACTION98.47
3.05-3.190.22031410.22292656X-RAY DIFFRACTION97.93
3.19-3.350.27711410.22272625X-RAY DIFFRACTION98.57
3.36-3.560.27841360.20932594X-RAY DIFFRACTION97.85
3.57-3.840.20061380.20012624X-RAY DIFFRACTION97.22
3.84-4.230.21361400.18932569X-RAY DIFFRACTION96.47
4.23-4.830.24371340.17692610X-RAY DIFFRACTION96.72
4.84-6.090.23561410.2072647X-RAY DIFFRACTION97.96
6.09-46.440.23831290.18772597X-RAY DIFFRACTION96.43
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)
12.42795036036-0.7174191713-0.4802871695712.29649767779-0.1566115360672.43031222337-0.12258848876-1.26919599255-0.2374639116970.4298847952520.302750410276-0.2175823099110.04546071747870.6321958517960.3385328667120.4675288349040.192789046942-0.0362841662521.00343352609-0.01279713387370.1971510674110.18834405720.9050797256428.6007754583
21.270372925190.3827252417730.4338413178180.652958710136-0.005227986066440.460990565806-0.17239353150.1020196553150.193358156404-0.1390833797870.06393905472820.0933773264209-0.124072133792-0.0867378367083-0.00297367221530.265386389787-0.0218056734978-0.01198573976830.163088772384-0.01550384290110.48780472835426.4864669619-1.98434490956-6.37970437966
30.659846862911-0.300615032696-0.1579539535140.2088789324180.007146781600620.0703977831772-0.4766129901570.01596678148560.366209502713-0.08102730641080.344389924510.232051157076-0.431138575271-0.00325893560289-0.0436449826780.532213288057-0.0566093865913-0.2354706458350.332209430196-0.01219768673031.1887606266616.84881163161.2255211538-11.430426312
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 371 )1 - 3711 - 371
22chain 'A' and (resid 1001 through 1136 )1001 - 1136372 - 511
33chain 'A' and (resid 1998 through 2015 )1998 - 2015512 - 529

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