[English] 日本語
Yorodumi
- EMDB-18810: Dimeric ternary structure of E6AP-E6-p53 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18810
TitleDimeric ternary structure of E6AP-E6-p53
Map dataSharpened map
Sample
  • Complex: Dimeric E6AP-E6-p53 ternary complex
    • Protein or peptide: Ubiquitin-protein ligase E3A
    • Protein or peptide: Ubiquitin-like protein SMT3,Protein E6
    • Protein or peptide: Cellular tumor antigen p53
  • Ligand: ZINC ION
KeywordsE3 ligase / viral protein / transcription factor / LIGASE
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / symbiont-mediated suppression of host transcription / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed ...sperm entry / positive regulation of Golgi lumen acidification / symbiont-mediated suppression of host transcription / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / prostate gland growth / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HECT-type E3 ubiquitin transferase / regulation of proteolysis / SUMOylation of RNA binding proteins / 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 / SUMOylation of chromatin organization proteins / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte 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 / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / progesterone receptor signaling pathway / ubiquitin-like protein ligase binding / androgen receptor signaling pathway / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / locomotory exploration behavior / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / protein sumoylation / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C
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) / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...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) / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein E6 / Cellular tumor antigen p53 / Ubiquitin-protein ligase E3A / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesHomo sapiens (human) / Human papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsSandate CR / Chakrabory D / Kater L / Kempf G / Thoma NH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2023
Title: Structural insights into viral hijacking of p53 by E6 and E6AP
Authors: Sandate CR / Chakraborty D / Kater L / Kempf G / Thoma NH
History
DepositionNov 1, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18810.png

Downloads & links

-
Map

FileDownload / File: emd_18810.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.68 Å
Density
Contour LevelBy AUTHOR: 0.393
Minimum - Maximum-2.0607047 - 3.5803647
Average (Standard dev.)-0.0011223054 (±0.09163551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_18810_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_18810_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_18810_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dimeric E6AP-E6-p53 ternary complex

EntireName: Dimeric E6AP-E6-p53 ternary complex
Components
  • Complex: Dimeric E6AP-E6-p53 ternary complex
    • Protein or peptide: Ubiquitin-protein ligase E3A
    • Protein or peptide: Ubiquitin-like protein SMT3,Protein E6
    • Protein or peptide: Cellular tumor antigen p53
  • Ligand: ZINC ION

-
Supramolecule #1: Dimeric E6AP-E6-p53 ternary complex

SupramoleculeName: Dimeric E6AP-E6-p53 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 352 KDa

-
Macromolecule #1: Ubiquitin-protein ligase E3A

MacromoleculeName: Ubiquitin-protein ligase E3A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.5955 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMEKLHQ CYWKSGEPQS DDIEASRMKR AAAKHLIERY YHQLTEGCGN EACTNEFCAS CPTFLRMDN NAAAIKALEL YKINAKLCDP HPSKKGASSA YLENSKGAPN NSCSEIKMNK KGARIDFKDV TYLTEEKVYE I LELCRERE ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMEKLHQ CYWKSGEPQS DDIEASRMKR AAAKHLIERY YHQLTEGCGN EACTNEFCAS CPTFLRMDN NAAAIKALEL YKINAKLCDP HPSKKGASSA YLENSKGAPN NSCSEIKMNK KGARIDFKDV TYLTEEKVYE I LELCRERE DYSPLIRVIG RVFSSAEALV QSFRKVKQHT KEELKSLQAK DEDKDEDEKE KAACSAAAME EDSEASSSRI GD SSQGDNN LQKLGPDDVS VDIDAIRRVY TRLLSNEKIE TAFLNALVYL SPNVECDLTY HNVYSRDPNY LNLFIIVMEN RNL HSPEYL EMALPLFCKA MSKLPLAAQG KLIRLWSKYN ADQIRRMMET FQQLITYKVI SNEFNSRNLV NDDDAIVAAS KCLK MVYYA NVVGGEVDTN HNEEDDEEPI PESSELTLQE LLGEERRNKK GPRVDPLETE LGVKTLDCRK PLIPFEEFIN EPLNE VLEM DKDYTFFKVE TENKFSFMTC PFILNAVTKN LGLYYDNRIR MYSERRITVL YSLVQGQQLN PYLRLKVRRD HIIDDA LVR LEMIAMENPA DLKKQLYVEF EGEQGVDEGG VSKEFFQLVV EEIFNPDIGM FTYDESTKLF WFNPSSFETE GQFTLIG IV LGLAIYNNCI LDVHFPMVVY RKLMGKKGTF RDLGDSHPVL YQSLKDLLEY EGNVEDDMMI TFQISQTDLF GNPMMYDL K ENGDKIPITN ENRKEFVNLY SDYILNKSVE KQFKAFRRGF HMVTNESPLK YLFRPEEIEL LICGSRNLDF QALEETTEY DGGYTRDSVL IREFWEIVHS FTDEQKRLFL QFTTGTDRAP VGGLGKLKMI IAKNGPDTER LPTSHTCFNV LLLPEYSSKE KLKERLLKA ITYAKGFGML

UniProtKB: Ubiquitin-protein ligase E3A

-
Macromolecule #2: Ubiquitin-like protein SMT3,Protein E6

MacromoleculeName: Ubiquitin-like protein SMT3,Protein E6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus type 16
Molecular weightTheoretical: 31.542988 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQTPED LDMEDNDII EAHREQIGGS ADENLYFQGM HQKRTAMFQD PQERPRKLPQ LCTELQTTIH DIILECVYCK QQLLRREVYD F AFRDLCIV ...String:
MSDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQTPED LDMEDNDII EAHREQIGGS ADENLYFQGM HQKRTAMFQD PQERPRKLPQ LCTELQTTIH DIILECVYCK QQLLRREVYD F AFRDLCIV YRDGNPYAVC DKCLKFYSKI SEYRHYSYSL YGTTLEQQYN KPLSDLLIRC INCQKPLSPE EKQRHLDKKQ RF HNIRGRW TGRCMSCSRS SRTRRETQL

UniProtKB: Ubiquitin-like protein SMT3, Protein E6

-
Macromolecule #3: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.495152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPR MPEAAPPVAP APAAPTPAAP APAPSWPLSS SVPSQKTYQG SYGFRLGFLH SGTAKSVTCT YSPALNKMFC Q LAKTCPVQ ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPR MPEAAPPVAP APAAPTPAAP APAPSWPLSS SVPSQKTYQG SYGFRLGFLH SGTAKSVTCT YSPALNKMFC Q LAKTCPVQ LWVDSTPPPG TRVRAMAIYK QSQHMTEVVR RCPHHERCSD SDGLAPPQHL IRVEGNLRVE YLDDRNTFRH SV VVPYEPP EVGSDCTTIH YNYMCNSSCM GGMNRRPILT IITLEDSSGN LLGRNSFEVR VCACPGRDRR TEEENLRKKG EPH HELPPG STKRALPNNT SSSPQPKKKP LDGEYFTLQI RGRERFEMFR ELNEALELKD AQAGKEPGGS RAHSSHLKSK KGQS TSRHK KLMFKTEGPD SD

UniProtKB: Cellular tumor antigen p53

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMKCl
0.5 mMMgCl2
0.5 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA current with Pelco EasyGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 47581 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 11300000
Startup modelType of model: OTHER / Details: Ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4) / Number images used: 85396
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8r1g:
Dimeric ternary structure of E6AP-E6-p53

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more