[English] 日本語
Yorodumi
- PDB-8uqt: Crystal structure of the Tree Shrew p53 tetramerization domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uqt
TitleCrystal structure of the Tree Shrew p53 tetramerization domain
ComponentsCellular tumor antigen p53
KeywordsTRANSCRIPTION / Tree Shrew p53 tetramerization domain stability
Function / homology
Function and homology information


protein tetramerization / PML body / rhythmic process / transcription cis-regulatory region binding / mitochondrial matrix / cell cycle / DNA-binding transcription factor activity / apoptotic process / endoplasmic reticulum / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesTupaia chinensis (Chinese tree shrew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsWahba, H.M. / Sakaguchi, S. / Nakagawa, N. / Wada, J. / Kamada, R. / Sakaguchi, K. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-03837 Canada
CitationJournal: Int J Mol Sci / Year: 2023
Title: Highly Similar Tetramerization Domains from the p53 Protein of Different Mammalian Species Possess Varying Biophysical, Functional and Structural Properties.
Authors: Sakaguchi, S. / Nakagawa, N. / Wahba, H.M. / Wada, J. / Kamada, R. / Omichinski, J.G. / Sakaguchi, K.
History
DepositionOct 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8553
Polymers7,7592
Non-polymers961
Water1,78399
1
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules

A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7106
Polymers15,5184
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area7230 Å2
ΔGint-78 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.871, 65.806, 32.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-512-

HOH

31A-527-

HOH

41A-546-

HOH

-
Components

#1: Protein/peptide Cellular tumor antigen p53


Mass: 3879.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tupaia chinensis (Chinese tree shrew) / Production host: Escherichia coli (E. coli) / References: UniProt: W8FSP6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.6 M Lithium sulfate monohydrate, 2% PEG 8000, 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→45.46 Å / Num. obs: 21880 / % possible obs: 91.7 % / Redundancy: 9.9 % / CC1/2: 1 / Net I/σ(I): 28.35
Reflection shellResolution: 1.16→1.201 Å / Num. unique obs: 21822 / CC1/2: 0.84

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→45.46 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 2005 9.16 %
Rwork0.1716 --
obs0.1732 21880 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 5 99 640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009544
X-RAY DIFFRACTIONf_angle_d1.154721
X-RAY DIFFRACTIONf_dihedral_angle_d12.925215
X-RAY DIFFRACTIONf_chiral_restr0.08274
X-RAY DIFFRACTIONf_plane_restr0.01195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.4061610.4228547X-RAY DIFFRACTION36
1.19-1.220.3379930.2717949X-RAY DIFFRACTION62
1.22-1.250.24041190.19371252X-RAY DIFFRACTION82
1.25-1.290.21021510.16391472X-RAY DIFFRACTION95
1.29-1.340.20541480.15571532X-RAY DIFFRACTION99
1.34-1.390.20491630.16441520X-RAY DIFFRACTION100
1.39-1.460.1761490.13661546X-RAY DIFFRACTION100
1.46-1.530.1551590.12461551X-RAY DIFFRACTION100
1.53-1.630.15051620.12951550X-RAY DIFFRACTION100
1.63-1.760.17071550.14111569X-RAY DIFFRACTION100
1.76-1.930.16171550.14821553X-RAY DIFFRACTION100
1.93-2.210.1681590.14711573X-RAY DIFFRACTION100
2.21-2.790.18071600.17231591X-RAY DIFFRACTION100
2.79-45.460.21161710.20981670X-RAY DIFFRACTION100

+
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