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- EMDB-63843: Structure of UBE3A-E6-p53 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63843
TitleStructure of UBE3A-E6-p53 complex
Map data
Sample
  • Complex: UBE3A-E6-p53 ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Protein E6
    • Protein or peptide: Cellular tumor antigen p53
    • Protein or peptide: Isoform I of Ubiquitin-protein ligase E3A
  • Ligand: ZINC ION
Keywordscomplex / PROTEIN BINDING
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 / 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 ...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 / 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 / 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 / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / transcription regulator activator activity / 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 / negative regulation of fibroblast proliferation / general transcription initiation factor binding / carbohydrate transmembrane transporter activity / positive regulation of execution phase of apoptosis / 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 / Regulation of TP53 Activity through Acetylation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / response to gamma radiation / protein K48-linked ubiquitination / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of TORC1 signaling / ATP-binding cassette (ABC) transporter complex / protein phosphatase 2A binding / molecular function activator activity / positive regulation of protein ubiquitination / transcription initiation-coupled chromatin remodeling / 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 / TP53 Regulates Metabolic Genes / brain development / autophagy / cell chemotaxis / 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 speciesHomo sapiens (human) / Human papillomavirus 16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsRen XK / Xin J / Liu JB / Chen SW / Yan KG / Liu XT / Zhang MJ
Funding support China, 5 items
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 XK / Xin J / Liu JB / Chen SW / Yan KG / Liu XT / Zhang MJ
History
DepositionMar 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63843.png

Downloads & links

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Map

FileDownload / File: emd_63843.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.67 Å/pix.
x 384 pix.
= 257.28 Å		0.67 Å/pix.
x 384 pix.
= 257.28 Å		0.67 Å/pix.
x 384 pix.
= 257.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.95
Minimum - Maximum-45.849110000000003 - 80.785300000000007
Average (Standard dev.)0.00021694429 (±1.1012369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 257.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : UBE3A-E6-p53 ternary complex

EntireName: UBE3A-E6-p53 ternary complex
Components
  • Complex: UBE3A-E6-p53 ternary complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Protein E6
    • Protein or peptide: Cellular tumor antigen p53
    • Protein or peptide: Isoform I of Ubiquitin-protein ligase E3A
  • Ligand: ZINC ION

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Supramolecule #1: UBE3A-E6-p53 ternary complex

SupramoleculeName: UBE3A-E6-p53 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Protein E6

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Protein E6
type: protein_or_peptide / ID: 1
Details: Recombinant Protein E6 with an N-terminal MBP-His-HRV 3C tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus 16
Molecular weightTheoretical: 61.225496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSHMHHHHH HSSGLEVLFQ GPGSMFQDPQ ERPR KLPQL CTELQTTIHD IILECVYCKQ QLLRREVYDF AFRDLCIVYR DGNPYAVCDK CLKFYSKISE YRHYSYSLYG TTLEQ QYNK PLSDLLIRCI NCQKPLSPEE KQRHLDKKQR FHNIRGRWTG RCMSCSRSSR TRRETQL

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Protein E6

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Macromolecule #2: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.865336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMEEPQSDP SVEPPLSQET FSDLWKLLPE NNVLSPLPSQ AMDDLMLSPD DIEQWFTEDP GPDEAPRMPE AAPPVAPAPA APTPAAPAP APSWPLSSSV PSQKTYQGSY GFRLGFLHSG TAKSVTCTYS PALNKMFCQL AKTCPVQLWV DSTPPPGTRV R AMAIYKQS ...String:
GPMEEPQSDP SVEPPLSQET FSDLWKLLPE NNVLSPLPSQ AMDDLMLSPD DIEQWFTEDP GPDEAPRMPE AAPPVAPAPA APTPAAPAP APSWPLSSSV PSQKTYQGSY GFRLGFLHSG TAKSVTCTYS PALNKMFCQL AKTCPVQLWV DSTPPPGTRV R AMAIYKQS QHMTEVVRRC PHHERCSDSD GLAPPQHLIR VEGNLRVEYL DDRNTFRHSV VVPYEPPEVG SDCTTIHYNY MC NSSCMGG MNRRPILTII TLEDSSGNLL GRNSFEVRVC ACPGRDRRTE EENLRKKGEP HHELPPGSTK RALPNNTSSS PQP KKKPLD GEYFTLQIRG RERFEMFREL NEALELKDAQ AGKEPGGSRA HSSHLKSKKG QSTSRHKKLM FKTEGPDSD

UniProtKB: Cellular tumor antigen p53

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Macromolecule #3: Isoform I of Ubiquitin-protein ligase E3A

MacromoleculeName: Isoform I of Ubiquitin-protein ligase E3A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.38582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSC SEIKMNKKGA RIDFKDVTYL TEEKVYEILE LCREREDYSP LIRVIGRVFS SAEALVQSFR KVKQHTKEEL K SLQAKDED ...String:
GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSC SEIKMNKKGA RIDFKDVTYL TEEKVYEILE LCREREDYSP LIRVIGRVFS SAEALVQSFR KVKQHTKEEL K SLQAKDED KDEDEKEKAA CSAAAMEEDS EASSSRIGDS SQGDNNLQKL GPDDVSVDID AIRRVYTRLL SNEKIETAFL NA LVYLSPN VECDLTYHNV YSRDPNYLNL FIIVMENRNL HSPEYLEMAL PLFCKAMSKL PLAAQGKLIR LWSKYNADQI RRM METFQQ LITYKVISNE FNSRNLVNDD DAIVAASKCL KMVYYANVVG GEVDTNHNEE DDEEPIPESS ELTLQELLGE ERRN KKGPR VDPLETELGV KTLDCRKPLI PFEEFINEPL NEVLEMDKDY TFFKVETENK FSFMTCPFIL NAVTKNLGLY YDNRI RMYS ERRITVLYSL VQGQQLNPYL RLKVRRDHII DDALVRLEMI AMENPADLKK QLYVEFEGEQ GVDEGGVSKE FFQLVV EEI FNPDIGMFTY DESTKLFWFN PSSFETEGQF TLIGIVLGLA IYNNCILDVH FPMVVYRKLM GKKGTFRDLG DSHPVLY QS LKDLLEYEGN VEDDMMITFQ ISQTDLFGNP MMYDLKENGD KIPITNENRK EFVNLYSDYI LNKSVEKQFK AFRRGFHM V TNESPLKYLF RPEEIELLIC GSRNLDFQAL EETTEYDGGY TRDSVLIREF WEIVHSFTDE QKRLFLQFTT GTDRAPVGG LGKLKMIIAK NGPDTERLPT SHTCFNVLLL PEYSSKEKLK ERLLKAITYA KGFGML

UniProtKB: Ubiquitin-protein ligase E3A

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111014
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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