[English] 日本語
Yorodumi
- PDB-2y9t: Structural basis of p63a SAM domain mutants involved in AEC syndrome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y9t
TitleStructural basis of p63a SAM domain mutants involved in AEC syndrome
ComponentsTUMOR PROTEIN 63
KeywordsAPOPTOSIS / STERILE ALPHA MOTIF / 5-HELIX BUNDLE
Function / homology
Function and homology information


positive regulation of somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / negative regulation of cellular senescence / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors ...positive regulation of somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / negative regulation of cellular senescence / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / WW domain binding / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Developmental Lineage of Mammary Gland Myoepithelial Cells / positive regulation of osteoblast differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / establishment of skin barrier / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / Notch signaling pathway / Pyroptosis / MDM2/MDM4 family protein binding / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / promoter-specific chromatin binding / p53 binding / spermatogenesis / regulation of apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / chromatin binding / DNA damage response / dendrite / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / DNA-templated transcription / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tumour protein p63, SAM domain / Transcription Factor, Ets-1 / : / 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 ...Tumour protein p63, SAM domain / Transcription Factor, Ets-1 / : / 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 / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS
AuthorsSathyamurthy, A. / Freund, S.M.V. / Johnson, C.M. / Allen, M.D.
CitationJournal: FEBS J. / Year: 2011
Title: Structural Basis of P63Alpha Sam Domain Mutants Involved in Aec Syndrome.
Authors: Sathyamurthy, A. / Freund, S.M.V. / Johnson, C.M. / Allen, M.D. / Bycroft, M.
History
DepositionFeb 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUMOR PROTEIN 63


Theoretical massNumber of molelcules
Total (without water)9,3311
Polymers9,3311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS > 0.25A
Representative

-
Components

#1: Protein TUMOR PROTEIN 63 / CHRONIC ULCERATIVE STOMATITIS PROTEIN / KERATINOCYTE TRANSCRIPTION FACTOR KET / TRANSFORMATION- ...CHRONIC ULCERATIVE STOMATITIS PROTEIN / KERATINOCYTE TRANSCRIPTION FACTOR KET / TRANSFORMATION-RELATED PROTEIN 63 / TUMOR PROTEIN P73-LIKE / P40 / P51 / P63 / CUSP / TP63 / P73L


Mass: 9330.511 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN, RESIDUES 543-622
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9H3D4
Sequence detailsGLY AND SER AND THE N-TERMINUS ARE FROM THE FUSION TAG

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Temperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
CNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS > 0.25A / Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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://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