[English] 日本語
Yorodumi
- PDB-1dxs: Crystal structure of the C-terminal sterile alpha motif (SAM) dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dxs
TitleCrystal structure of the C-terminal sterile alpha motif (SAM) domain of human p73 alpha splice variant
ComponentsP53-LIKE TRANSCRIPTION FACTOR
KeywordsGENE REGULATION / P73 SAM-LIKE DOMAIN / P53 P63 HOMOLOGUE / STERILE ALPHA MOTIF / TUMOUR SUPRESSOR
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis ...positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell size / neuron development / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / release of cytochrome c from mitochondria / transcription corepressor binding / post-embryonic development / hippocampus development / protein tetramerization / kidney development / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of MAPK cascade / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / inflammatory response / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / centrosome / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p73, 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 ...Tumour protein p73, 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWang, W.K. / Chen, Y.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the C-Terminal Sterile Alpha-Motif (Sam) Domain of Human P73 Alpha
Authors: Wang, W.K. / Bycroft, M. / Foster, N.W. / Buckle, A.M. / Fersht, A.R. / Chen, Y.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Studies of a Sam Domain at the C-Terminus of Human P73 Alpha
Authors: Wang, W.K. / Proctor, M. / Buckle, A.M. / Bycroft, M. / Chen, Y.W.
#2: Journal: Embo J. / Year: 1999
Title: Solution Structure of a Conserved C-Terminal Domain of P73 with Structural Homology to the Sam Domain
Authors: Chi, S.-W. / Ayed, A. / Arrowsmith, C.H.
History
DepositionJan 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 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 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.6Dec 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P53-LIKE TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)9,0261
Polymers9,0261
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.020, 32.020, 133.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-3019-

HOH

21A-3021-

HOH

DetailsBIOLOGICAL_UNIT: MONOMER

-
Components

#1: Protein P53-LIKE TRANSCRIPTION FACTOR


Mass: 9026.124 Da / Num. of mol.: 1 / Fragment: C-TERMINAL STERILE ALPHA MOTIF (SAM) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUS / Gene: P73 / Plasmid: MODIFIED PRESET A / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O15350
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES GLY-SER (-2 TO -1) CLONING ARTIFACT

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALLIZED IN 0.1M TRIS-HCL PH8.5, 2.0M MONO-AMMONIUM DIHYDROGEN PHOSPHATE, AT 290K., pH 8.50
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Details: Wang, W.K., (2000) Acta Crystallogr.,Sect.D, 56, 769.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
32.0 Mammonium dihydrogen orthophosphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→26 Å / Num. obs: 2510 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Net I/σ(I): 7.6
Reflection shellResolution: 2.54→2.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2 / Rsym value: 0.377 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
CNS0.9refinement
iMOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COK

1cok


Resolution: 2.54→26 Å / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: C TERMINAL RESIDUES ARE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.346 269 10.2 %RANDOM
Rwork0.275 ---
obs0.275 2510 94.9 %-
Solvent computationSolvent model: MASKED FLAT MODEL / Bsol: 92.7 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.93 Å20 Å20 Å2
2---9.93 Å20 Å2
3---19.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.54→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms441 0 0 26 467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.8
X-RAY DIFFRACTIONc_mcangle_it12.1
X-RAY DIFFRACTIONc_scbond_it14
X-RAY DIFFRACTIONc_scangle_it19.4
LS refinement shellResolution: 2.54→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.483 32 12.9 %
Rwork0.351 207 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9A / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

+
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