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- PDB-9u4d: Structure of UBE3A-E6-p53 complex -

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Basic information

Entry
Database: PDB / ID: 9u4d
TitleStructure of UBE3A-E6-p53 complex
Components
  • Cellular tumor antigen p53
  • Isoform I of Ubiquitin-protein ligase E3A
  • Maltose/maltodextrin-binding periplasmic protein,Protein E6
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / regulation of ubiquitin-dependent protein catabolic process / Golgi lumen acidification / symbiont-mediated suppression of host apoptosis / HECT-type E3 ubiquitin transferase / negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition ...symbiont-mediated suppression of host transcription / regulation of ubiquitin-dependent protein catabolic process / Golgi lumen acidification / symbiont-mediated suppression of host apoptosis / HECT-type E3 ubiquitin transferase / negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / transcription regulator activator activity / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / regulation of Cdc42 protein signal transduction / circadian behavior / cellular response to actinomycin D / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / detection of maltose stimulus / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / progesterone receptor signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / response to progesterone / carbohydrate transport / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / replicative senescence / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of proteolysis / viral process / positive regulation of intrinsic apoptotic signaling pathway / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / carbohydrate transmembrane transporter activity / type II interferon-mediated signaling pathway / postsynaptic cytosol / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / response to gamma radiation / 14-3-3 protein binding / protein K48-linked ubiquitination / MDM2/MDM4 family protein binding / negative regulation of TORC1 signaling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ATP-binding cassette (ABC) transporter complex / protein phosphatase 2A binding / molecular function activator activity / transcription initiation-coupled chromatin remodeling / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / DNA damage response, signal transduction by p53 class mediator / brain development / TP53 Regulates Metabolic Genes / cell chemotaxis / autophagy / TP53 Regulates Transcription of DNA Repair Genes
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 / 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 / p53-like transcription factor, DNA-binding / 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
Protein E6 / Cellular tumor antigen p53 / Maltose/maltodextrin-binding periplasmic protein / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human papillomavirus 16
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsRen, X.K. / Xin, J. / Liu, J.B. / Chen, S.W. / Yan, K.G. / Liu, X.T. / Zhang, M.J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
Other government2023B0303010001
Other government2021ZT09Y104
Other governmentKQTD20210811090115021
Other governmentA2303054
CitationJournal: To Be Published
Title: Structure of UBE3A-E6-p53 complex
Authors: Ren, X.K. / Xin, J. / Liu, J.B. / Chen, S.W. / Yan, K.G. / Liu, X.T. / Zhang, M.J.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Maltose/maltodextrin-binding periplasmic protein,Protein E6
C: Cellular tumor antigen p53
A: Isoform I of Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,6736
Polymers203,4773
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 61225.496 Da / Num. of mol.: 1 / Mutation: C87S,C104S,C118S,C147S
Source method: isolated from a genetically manipulated source
Details: Recombinant Protein E6 with an N-terminal MBP-His-HRV 3C tag
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Human papillomavirus 16
Gene: malE, b4034, JW3994, E6 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P03126
#2: Protein Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 43865.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#3: Protein Isoform I of Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...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: 98385.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli (E. coli)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: UBE3A-E6-p53 ternary complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Human papillomavirus 16333760
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111014 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237743
ELECTRON MICROSCOPYf_angle_d0.5210461
ELECTRON MICROSCOPYf_chiral_restr0.03921138
ELECTRON MICROSCOPYf_plane_restr0.00371363
ELECTRON MICROSCOPYf_dihedral_angle_d3.38161036

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