[English] 日本語
Yorodumi
- PDB-2wqj: Crystal structure of a truncated variant of the human p73 tetrame... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wqj
TitleCrystal structure of a truncated variant of the human p73 tetramerization domain
ComponentsTUMOR PROTEIN P73P73
KeywordsTRANSCRIPTION / P73 / P63 / P53 / TUMOR SUPPRESSION / TRANSCRIPTION FACTOR / TETRAMER / HEXAMER / OLIGOMERIZATION DOMAIN / DNA-BINDING / COOPERATIVITY / CELL-CYCLE CONTROL / TRANSCRIPTION REGULATION / APOPTOSIS / CELL CYCLE / DEVELOPMENT
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / 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 oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / 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 oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / mismatch repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Tumour protein p73, SAM domain / 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) ...Tumour protein p73, SAM domain / 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
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoerger, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural Evolution of P53, P63, and P73: Implication for Heterotetramer Formation.
Authors: Joerger, A.C. / Rajagopalan, S. / Natan, E. / Veprintsev, D.B. / Robinson, C.V. / Fersht, A.R.
History
DepositionAug 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUMOR PROTEIN P73
B: TUMOR PROTEIN P73
C: TUMOR PROTEIN P73
D: TUMOR PROTEIN P73
E: TUMOR PROTEIN P73
F: TUMOR PROTEIN P73
G: TUMOR PROTEIN P73
H: TUMOR PROTEIN P73
I: TUMOR PROTEIN P73
J: TUMOR PROTEIN P73
K: TUMOR PROTEIN P73
L: TUMOR PROTEIN P73
M: TUMOR PROTEIN P73
N: TUMOR PROTEIN P73
O: TUMOR PROTEIN P73
P: TUMOR PROTEIN P73
Q: TUMOR PROTEIN P73
R: TUMOR PROTEIN P73
S: TUMOR PROTEIN P73
T: TUMOR PROTEIN P73
U: TUMOR PROTEIN P73
V: TUMOR PROTEIN P73
W: TUMOR PROTEIN P73
X: TUMOR PROTEIN P73
Y: TUMOR PROTEIN P73
Z: TUMOR PROTEIN P73
1: TUMOR PROTEIN P73
2: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)117,00528
Polymers117,00528
Non-polymers00
Water8,125451
1
G: TUMOR PROTEIN P73
H: TUMOR PROTEIN P73
I: TUMOR PROTEIN P73
J: TUMOR PROTEIN P73
K: TUMOR PROTEIN P73
L: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-79.67 kcal/mol
Surface area9220 Å2
MethodPISA
2
A: TUMOR PROTEIN P73
B: TUMOR PROTEIN P73
C: TUMOR PROTEIN P73
D: TUMOR PROTEIN P73
E: TUMOR PROTEIN P73
F: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-73.53 kcal/mol
Surface area10120 Å2
MethodPISA
3
S: TUMOR PROTEIN P73
T: TUMOR PROTEIN P73
U: TUMOR PROTEIN P73
V: TUMOR PROTEIN P73
W: TUMOR PROTEIN P73
X: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-80.48 kcal/mol
Surface area9330 Å2
MethodPISA
4
M: TUMOR PROTEIN P73
N: TUMOR PROTEIN P73
O: TUMOR PROTEIN P73
P: TUMOR PROTEIN P73
Q: TUMOR PROTEIN P73
R: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-73.62 kcal/mol
Surface area9750 Å2
MethodPISA
5
Y: TUMOR PROTEIN P73
Z: TUMOR PROTEIN P73
1: TUMOR PROTEIN P73
2: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)16,7154
Polymers16,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-49.2 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.850, 98.930, 120.120
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide ...
TUMOR PROTEIN P73 / P73 / P53-LIKE TRANSCRIPTION FACTOR / P53-RELATED PROTEIN / P73


Mass: 4178.738 Da / Num. of mol.: 28
Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 351-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O15350
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWO ADDITIONAL N-TERMINAL RESIDUES (GS CLONING TAG)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 10 MG/ML IN 20 MM TRIS (PH 8.5), 50 MM NACL. CRYSTALLIZATION BUFFER: 0.1 M TRIS (PH 8.5), 0.9 M AMMONIUM PHOSPHATE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→76.4 Å / Num. obs: 90937 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→24.96 Å / SU ML: 0.29 / σ(F): 1.08 / Phase error: 25.49 / Stereochemistry target values: ML
Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ...Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ARCHITECTURE OF THE P73 TETRAMER. SEE PDB ENTRY 2WQI WITH THE STRUCTURE OF P73 RESIDUES 351-399 FOR COMPARISON.
RfactorNum. reflection% reflection
Rfree0.2484 8569 4.9 %
Rwork0.2103 --
obs0.2123 173614 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.14 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.9256 Å20 Å2-1.0093 Å2
2--3.6417 Å20 Å2
3----6.5673 Å2
Refinement stepCycle: LAST / Resolution: 2→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 0 451 7100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066711
X-RAY DIFFRACTIONf_angle_d0.8928939
X-RAY DIFFRACTIONf_dihedral_angle_d15.0762620
X-RAY DIFFRACTIONf_chiral_restr0.055997
X-RAY DIFFRACTIONf_plane_restr0.0031120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.31432240.27115290X-RAY DIFFRACTION94
2.0227-2.04650.29162660.26415412X-RAY DIFFRACTION95
2.0465-2.07150.30322700.26775406X-RAY DIFFRACTION94
2.0715-2.09770.29792740.24115357X-RAY DIFFRACTION95
2.0977-2.12530.2342910.23345424X-RAY DIFFRACTION95
2.1253-2.15440.28512870.23325412X-RAY DIFFRACTION95
2.1544-2.18510.26593280.22875312X-RAY DIFFRACTION95
2.1851-2.21770.31043100.24045469X-RAY DIFFRACTION95
2.2177-2.25230.25222480.23315448X-RAY DIFFRACTION95
2.2523-2.28920.33192570.23715504X-RAY DIFFRACTION96
2.2892-2.32870.25992400.23845442X-RAY DIFFRACTION96
2.3287-2.3710.3083360.23365405X-RAY DIFFRACTION96
2.371-2.41660.25842760.22695525X-RAY DIFFRACTION96
2.4166-2.46590.28352780.2235431X-RAY DIFFRACTION96
2.4659-2.51940.2642880.22635539X-RAY DIFFRACTION96
2.5194-2.5780.28182960.22255455X-RAY DIFFRACTION97
2.578-2.64240.23952730.21255512X-RAY DIFFRACTION97
2.6424-2.71370.27992770.2155513X-RAY DIFFRACTION97
2.7137-2.79350.25642620.21315595X-RAY DIFFRACTION97
2.7935-2.88350.25812830.21165519X-RAY DIFFRACTION97
2.8835-2.98640.25222870.21985530X-RAY DIFFRACTION97
2.9864-3.10580.26612900.22315608X-RAY DIFFRACTION98
3.1058-3.24680.223040.21055541X-RAY DIFFRACTION98
3.2468-3.41760.23673320.19275599X-RAY DIFFRACTION99
3.4176-3.63110.19983100.17035603X-RAY DIFFRACTION99
3.6311-3.91050.21513200.17445577X-RAY DIFFRACTION99
3.9105-4.30230.21013040.17675606X-RAY DIFFRACTION99
4.3023-4.92070.19832970.17075666X-RAY DIFFRACTION99
4.9207-6.18390.2632750.21915671X-RAY DIFFRACTION99
6.1839-24.96240.26262860.22765674X-RAY DIFFRACTION99

+
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