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- PDB-3py7: Crystal structure of full-length Bovine Papillomavirus oncoprotei... -

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Entry
Database: PDB / ID: 3py7
TitleCrystal structure of full-length Bovine Papillomavirus oncoprotein E6 in complex with LD1 motif of paxillin at 2.3A resolution
Componentsmaltose-binding periplasmic protein,paxillin LD1,protein E6 chimera
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


: / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / detection of maltose stimulus / maltose binding ...: / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / : / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / lamellipodium / outer membrane-bounded periplasmic space / cell cortex / protein phosphatase binding / host cell cytoplasm / periplasmic space / cell adhesion / focal adhesion / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA damage response / host cell nucleus / regulation of DNA-templated transcription / signal transduction / DNA binding / zinc ion binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Paxillin / : / : / Paxillin family / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...Paxillin / : / : / Paxillin family / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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-maltotriose / Protein E6 / Maltose/maltodextrin-binding periplasmic protein / Paxillin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
bovine papillomavirus type 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.288 Å
AuthorsCavarelli, J.
CitationJournal: Science / Year: 2013
Title: Structural basis for hijacking of cellular LxxLL motifs by papillomavirus E6 oncoproteins.
Authors: Zanier, K. / Charbonnier, S. / Sidi, A.O. / McEwen, A.G. / Ferrario, M.G. / Poussin-Courmontagne, P. / Cura, V. / Brimer, N. / Babah, K.O. / Ansari, T. / Muller, I. / Stote, R.H. / ...Authors: Zanier, K. / Charbonnier, S. / Sidi, A.O. / McEwen, A.G. / Ferrario, M.G. / Poussin-Courmontagne, P. / Cura, V. / Brimer, N. / Babah, K.O. / Ansari, T. / Muller, I. / Stote, R.H. / Cavarelli, J. / Vande Pol, S. / Trave, G.
History
DepositionDec 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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-binding periplasmic protein,paxillin LD1,protein E6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3894
Polymers57,7541
Non-polymers6353
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.051, 123.090, 94.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein maltose-binding periplasmic protein,paxillin LD1,protein E6 chimera


Mass: 57753.816 Da / Num. of mol.: 1
Mutation: D108A,K109A,K265A,E385A,K388A,D389A (maltose-binding periplasmic protein)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) bovine papillomavirus type 1, (gene. exp.) Homo sapiens (human)
Gene: malE,PXN,E6 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: P49023, UniProt: P06931
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][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: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A IS A TRIPLE CHIMERA: MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 27-392), ENGINEERED ...CHAIN A IS A TRIPLE CHIMERA: MALTOSE-BINDING PERIPLASMIC PROTEIN (UNP RESIDUES 27-392), ENGINEERED LINKER, PAXILLIN LD1 (UNP RESIDUES 1-10), ENGINEERED LINKER, PROTEIN E6

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 2% PEG2000 MME 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2009
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.288→40 Å / Num. all: 28033 / Num. obs: 27781 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 33.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1380 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.288→39.953 Å / SU ML: 0.27 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1376 5.01 %
Rwork0.1866 --
obs0.1885 27450 97.91 %
all-28036 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.427 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7787 Å20 Å2-0 Å2
2--5.5863 Å20 Å2
3----0.8076 Å2
Refinement stepCycle: LAST / Resolution: 2.288→39.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 36 186 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074002
X-RAY DIFFRACTIONf_angle_d0.9265432
X-RAY DIFFRACTIONf_dihedral_angle_d16.0361471
X-RAY DIFFRACTIONf_chiral_restr0.064602
X-RAY DIFFRACTIONf_plane_restr0.005699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2876-2.36930.29661100.21292405X-RAY DIFFRACTION91
2.3693-2.46420.23651480.20652531X-RAY DIFFRACTION97
2.4642-2.57630.29031380.21962571X-RAY DIFFRACTION98
2.5763-2.71210.25251220.21912621X-RAY DIFFRACTION99
2.7121-2.8820.26961270.21482639X-RAY DIFFRACTION99
2.882-3.10440.26541590.21352628X-RAY DIFFRACTION100
3.1044-3.41670.25561440.2032628X-RAY DIFFRACTION100
3.4167-3.91070.20111220.17322696X-RAY DIFFRACTION100
3.9107-4.92570.17011500.14462681X-RAY DIFFRACTION100
4.9257-39.95920.21831560.18852674X-RAY DIFFRACTION96
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)
10.9692-0.6042-0.16831.05260.08440.63430.01320.03910.1227-0.05080.00960.0139-0.0394-0.025700.2448-0.0345-0.02180.28880.01670.268635.164937.09699.8181
20.45930.2097-0.03910.3414-0.02020.4754-0.0352-0.1135-0.07680.0031-0.00450.1420.0949-0.0113-00.3553-0.01210.04360.2665-0.01570.333440.73610.51628.8751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1residues 3:382 and chain AA3 - 382
2X-RAY DIFFRACTION2residues 397:516 and chain AA397 - 516

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