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Basic information

Entry
Database: PDB / ID: 4giz
TitleCrystal structure of full-length human papillomavirus oncoprotein E6 in complex with LXXLL peptide of ubiquitin ligase E6AP at 2.55 A resolution
Components
  • Maltose-binding periplasmic protein, UBIQUITIN LIGASE EA6P: chimeric protein
  • Protein E6
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / symbiont-mediated suppression of host transcription / motor learning / regulation of ubiquitin-dependent protein catabolic process / symbiont-mediated perturbation of host apoptosis / prostate gland growth / HECT-type E3 ubiquitin transferase / regulation of proteolysis ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / symbiont-mediated suppression of host transcription / motor learning / regulation of ubiquitin-dependent protein catabolic process / symbiont-mediated perturbation of host apoptosis / prostate gland growth / HECT-type E3 ubiquitin transferase / regulation of proteolysis / activation of GTPase activity / detection of maltose stimulus / maltose transport complex / androgen receptor signaling pathway / locomotory exploration behavior / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein autoubiquitination / protein K48-linked ubiquitination / progesterone receptor signaling pathway / ovarian follicle development / negative regulation of TORC1 signaling / cellular response to brain-derived neurotrophic factor stimulus / proteasome complex / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of protein ubiquitination / response to cocaine / response to progesterone / PDZ domain binding / brain development / regulation of circadian rhythm / response to hydrogen peroxide / regulation of synaptic plasticity / 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 / 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / DNA damage response / glutamatergic synapse / host cell nucleus / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
E6 early regulatory protein / CRO Repressor / 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) ...E6 early regulatory protein / CRO Repressor / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltohexaose / Protein E6 / Maltose/maltodextrin-binding periplasmic protein / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
HOMO SAPIENS (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMcEwen, A.G. / Zanier, K. / Charbonnier, S. / Poussin, P. / Cura, V. / Vande Pol, S. / Trave, G. / Cavarelli, 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
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
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_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_atom_id / _atom_site.label_comp_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_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.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 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, UBIQUITIN LIGASE EA6P: chimeric protein
B: Maltose-binding periplasmic protein, UBIQUITIN LIGASE EA6P: chimeric protein
C: Protein E6
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,85910
Polymers117,6164
Non-polymers2,2436
Water10,305572
1
A: Maltose-binding periplasmic protein, UBIQUITIN LIGASE EA6P: chimeric protein
C: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9295
Polymers58,8082
Non-polymers1,1223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-5 kcal/mol
Surface area23200 Å2
MethodPISA
2
B: Maltose-binding periplasmic protein, UBIQUITIN LIGASE EA6P: chimeric protein
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9295
Polymers58,8082
Non-polymers1,1223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-12 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.279, 134.936, 138.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICALLY RELEVANT QUATERNARY STRUCTURE OF E6 PV REMAIN TO BE PROVEN. THE INDICATED BIOLOGIAL DIMER IS NOT PROVEN YET

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Components

#1: Protein Maltose-binding periplasmic protein, UBIQUITIN LIGASE EA6P: chimeric protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 41672.055 Da / Num. of mol.: 2 / Fragment: unp residues 27-392/403-414 / Mutation: D83A,K84A,K240A,E360A,D364A,K363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) HOMO SAPIENS (human)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q05086
#2: Protein Protein E6


Mass: 17135.740 Da / Num. of mol.: 2 / Fragment: unp residues 9-150 / Mutation: F47R,C80S,C97S,C111S,C140S
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-(1-4)-alpha-D-glucopyranose / alpha-maltohexaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 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]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF RESIDUES A372 TO A383 (AND B372 TO B383) CORRESPOND THE PEPTIDE CONTAINING RESIDUES 403 ...SEQUENCE OF RESIDUES A372 TO A383 (AND B372 TO B383) CORRESPOND THE PEPTIDE CONTAINING RESIDUES 403 TO 414 OF UBIQUITUIN LIGASE EA6P. EA6P UBIQUITUIN-PROTEIN LIGASE E3A, HOMO SAPIENS, UNIPROT Q05086 (UBE3A_HUMAN), ISOFORM III

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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: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 10% peg8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2010
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.55→37.33 Å / Num. obs: 65602 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 62.47 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 31
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.537 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→37.33 Å / Cor.coef. Fo:Fc: 0.9443 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 3325 5.07 %RANDOM
Rwork0.1662 ---
obs0.1677 65602 99.87 %-
all-65687 --
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--15.1856 Å20 Å20 Å2
2--9.5904 Å20 Å2
3---5.5951 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 2.55→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8282 0 138 572 8992
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098666HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0611772HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2966SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes238HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it8666HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2458 243 5.05 %
Rwork0.2057 4568 -
all0.2076 4811 -
obs--99.87 %
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)
11.0418-0.92290.51211.6493-0.35020.55290.0249-0.0453-0.0870.0296-0.00290.0360.05050.0097-0.022-0.01460.00870.0254-0.1206-0.0106-0.0918-0.805326.619936.5647
21.5128-0.34240.85920.4193-0.20781.28160.0020.24960.0487-0.0688-0.0182-0.0118-0.00880.06460.0162-0.022-0.0304-0.0151-0.047-0.0082-0.1433-25.595767.9666-8.4137
31.1457-0.34520.73461.1704-0.93534.455-0.0780.04110.04610.0643-0.03-0.2256-0.10830.45780.108-0.09210.01170.0067-0.0899-0.0353-0.03083.816359.934830.3565
40.9031-0.1830.30173.4269-0.51131.2468-0.03940.04170.0808-0.0405-0.03020.4935-0.054-0.15870.0696-0.11880.0014-0.0414-0.06-0.0472-0.0067-30.414464.509825.2946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|383 A|400 - A|400 }A2 - 383
2X-RAY DIFFRACTION1{ A|2 - A|383 A|400 - A|400 }A400
3X-RAY DIFFRACTION2{ B|2 - B|383 B|400 - B|400 }B2 - 383
4X-RAY DIFFRACTION2{ B|2 - B|383 B|400 - B|400 }B400
5X-RAY DIFFRACTION3{ C|2 - C|143 C|201 - C|202 }C2 - 143
6X-RAY DIFFRACTION3{ C|2 - C|143 C|201 - C|202 }C201 - 202
7X-RAY DIFFRACTION4{ D|2 - D|143 D|201 - D|202 }D2 - 143
8X-RAY DIFFRACTION4{ D|2 - D|143 D|201 - D|202 }D201 - 202

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