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- PDB-4xr8: Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.2... -

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Basic information

Entry
Database: PDB / ID: 4xr8
TitleCrystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
Components
  • Cellular tumor antigen p53P53
  • Maltose-binding periplasmic protein, ubiquitin ligase E6AP
  • Protein E6
KeywordsVIRAL PROTEIN/ ANTITUMOR PROTEIN / Human papillomavirus 16 / E6 oncoprotein / Ubiquitin-Ligase E6AP / tumor suppressor p53 / p53 degradation / viral protein-antitumor protein / VIRAL PROTEIN- ANTITUMOR PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / detection of maltose stimulus / maltose binding / maltose transport complex / negative regulation of DNA replication / ER overload response / maltose transport / B cell lineage commitment / thymocyte apoptotic process / maltodextrin transmembrane transport / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / carbohydrate transmembrane transporter activity / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / carbohydrate transport / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis
Similarity search - Function
E6 early regulatory protein / CRO Repressor / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif ...E6 early regulatory protein / CRO Repressor / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / p53-like transcription factor, DNA-binding / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / DI(HYDROXYETHYL)ETHER / Protein E6 / Cellular tumor antigen p53 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
HOMO SAPIENS (human)
Homo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMartinez-Zapien, D. / Ruiz, F.X. / Mitschler, A. / Podjarny, A. / Trave, G. / Zanier, K.
CitationJournal: Nature / Year: 2016
Title: Structure of the E6/E6AP/p53 complex required for HPV-mediated degradation of p53.
Authors: Martinez-Zapien, D. / Ruiz, F.X. / Poirson, J. / Mitschler, A. / Ramirez, J. / Forster, A. / Cousido-Siah, A. / Masson, M. / Pol, S.V. / Podjarny, A. / Trave, G. / Zanier, K.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: 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_assembly_gen / 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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-binding periplasmic protein, ubiquitin ligase E6AP
B: Maltose-binding periplasmic protein, ubiquitin ligase E6AP
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
F: Protein E6
H: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,66919
Polymers165,1066
Non-polymers1,56413
Water6,377354
1
A: Maltose-binding periplasmic protein, ubiquitin ligase E6AP
C: Cellular tumor antigen p53
F: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,36610
Polymers82,5533
Non-polymers8137
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein, ubiquitin ligase E6AP
D: Cellular tumor antigen p53
H: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3049
Polymers82,5533
Non-polymers7516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.842, 128.939, 81.560
Angle α, β, γ (deg.)90.00, 92.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ABCDFH

#1: Protein Maltose-binding periplasmic protein, ubiquitin ligase E6AP / MBP / MMBP / Maltodextrin-binding protein


Mass: 41803.258 Da / Num. of mol.: 2 / 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 K-12 (bacteria) / References: UniProt: P0AEX9
#2: Protein Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22448.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P04637
#3: Protein Protein E6


Mass: 18301.107 Da / Num. of mol.: 2 / Mutation: 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 K-12 (bacteria) / References: UniProt: P03126

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Sugars , 1 types, 2 molecules

#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 365 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 7.5 % PEG 20K, 0.05 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 77282 / % possible obs: 98.56 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.52
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.99 / % possible all: 89.64

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIZ, 1TUP

4giz

1tup


Resolution: 2.25→49.635 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 3868 5.01 %Random 5%
Rwork0.1936 ---
obs0.1962 77274 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→49.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11494 0 84 354 11932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111941
X-RAY DIFFRACTIONf_angle_d1.34816177
X-RAY DIFFRACTIONf_dihedral_angle_d14.4294528
X-RAY DIFFRACTIONf_chiral_restr0.0531755
X-RAY DIFFRACTIONf_plane_restr0.0072106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2284-2.25560.35511000.29571896X-RAY DIFFRACTION71
2.2556-2.28420.34451430.28362643X-RAY DIFFRACTION100
2.2842-2.31420.32351540.27942626X-RAY DIFFRACTION100
2.3142-2.34590.36951340.27092653X-RAY DIFFRACTION100
2.3459-2.37940.31891400.25892622X-RAY DIFFRACTION100
2.3794-2.41490.27421320.23782669X-RAY DIFFRACTION100
2.4149-2.45270.30291400.24252638X-RAY DIFFRACTION100
2.4527-2.49290.29531650.23912628X-RAY DIFFRACTION100
2.4929-2.53590.2921250.24072669X-RAY DIFFRACTION100
2.5359-2.5820.33021360.23752644X-RAY DIFFRACTION100
2.582-2.63160.29891140.23412699X-RAY DIFFRACTION100
2.6316-2.68540.27631610.22692615X-RAY DIFFRACTION100
2.6854-2.74370.2921450.22862637X-RAY DIFFRACTION100
2.7437-2.80760.32451320.23592652X-RAY DIFFRACTION100
2.8076-2.87780.34311490.24152673X-RAY DIFFRACTION100
2.8778-2.95560.30361320.23772599X-RAY DIFFRACTION100
2.9556-3.04250.28961190.24122688X-RAY DIFFRACTION100
3.0425-3.14070.3211460.23592673X-RAY DIFFRACTION100
3.1407-3.25290.28221310.2192635X-RAY DIFFRACTION99
3.2529-3.38320.25681350.21142600X-RAY DIFFRACTION98
3.3832-3.53710.27721450.20892637X-RAY DIFFRACTION99
3.5371-3.72350.25181410.19592648X-RAY DIFFRACTION100
3.7235-3.95670.22521480.17462635X-RAY DIFFRACTION100
3.9567-4.26210.18481560.15672642X-RAY DIFFRACTION100
4.2621-4.69070.17961420.1452667X-RAY DIFFRACTION100
4.6907-5.36870.20221240.14782685X-RAY DIFFRACTION100
5.3687-6.76130.22561430.16762657X-RAY DIFFRACTION99
6.7613-49.64730.17451360.14282676X-RAY DIFFRACTION98

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