[English] 日本語
Yorodumi
- EMDB-1141: The structure of p53 tumour suppressor protein reveals the basis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1141
TitleThe structure of p53 tumour suppressor protein reveals the basis for its functional plasticity.
Map dataThe EM map of the p53 tumour suppressor
Sample
  • Sample: murine p53
  • Protein or peptide: p53
Function / homologyp53 tumour suppressor family / nucleus
Function and homology information
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.7 Å
AuthorsOkorokov AL / Sherman MB / Milner J / Orlova EV
CitationJournal: EMBO J / Year: 2006
Title: The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity.
Authors: Andrei L Okorokov / Michael B Sherman / Celia Plisson / Vera Grinkevich / Kristmundur Sigmundsson / Galina Selivanova / Jo Milner / Elena V Orlova /
Abstract: p53 major tumour suppressor protein has presented a challenge for structural biology for two decades. The intact and complete p53 molecule has eluded previous attempts to obtain its structure, ...p53 major tumour suppressor protein has presented a challenge for structural biology for two decades. The intact and complete p53 molecule has eluded previous attempts to obtain its structure, largely due to the intrinsic flexibility of the protein. Using ATP-stabilised p53, we have employed cryoelectron microscopy and single particle analysis to solve the first three-dimensional structure of the full-length p53 tetramer (resolution 13.7 A). The p53 molecule is a D2 tetramer, resembling a hollow skewed cube with node-like vertices of two sizes. Four larger nodes accommodate central core domains, as was demonstrated by fitting of its X-ray structure. The p53 monomers are connected via their juxtaposed N- and C-termini within smaller N/C nodes to form dimers. The dimers form tetramers through the contacts between core nodes and N/C nodes. This structure revolutionises existing concepts of p53's molecular organisation and resolves conflicting data relating to its biochemical properties. This architecture of p53 in toto suggests novel mechanisms for structural plasticity, which enables the protein to bind variably spaced DNA target sequences, essential for p53 transactivation and tumour suppressor functions.
History
DepositionJul 28, 2005-
Header (metadata) releaseJul 28, 2005-
Map releaseJul 28, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1141.gif

Downloads & links

-
Map

FileDownload / File: emd_1141.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of the p53 tumour suppressor
Voxel sizeX=Y=Z: 1.5 Å
Density
Contour Level1: 0.0313 / Movie #1: 0.017
Minimum - Maximum-0.0157751 - 0.115924
Average (Standard dev.)0.00353103 (±0.0127307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 192 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z192.000192.000192.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0160.1160.004

-
Supplemental data

-
Sample components

-
Entire : murine p53

EntireName: murine p53
Components
  • Sample: murine p53
  • Protein or peptide: p53

-
Supramolecule #1000: murine p53

SupramoleculeName: murine p53 / type: sample / ID: 1000 / Details: homogenous sample / Oligomeric state: tetramer / Number unique components: 1
Molecular weightExperimental: 180 KDa / Theoretical: 174 KDa / Method: ultracentrifugation

-
Macromolecule #1: p53

MacromoleculeName: p53 / type: protein_or_peptide / ID: 1 / Name.synonym: tumour suppressor / Details: ATP-g-S complex / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse / Organelle: nucleus
Molecular weightExperimental: 43 KDa / Theoretical: 45 KDa
Recombinant expressionOrganism: Baculoviral system in Sf9 insect cells / Recombinant plasmid: pVL1393
SequenceGO: nucleus / InterPro: p53 tumour suppressor family

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 150mM NaCl, 5mM MgCl2, 25mM Tris-HCl
GridDetails: R2/2 quantifoilMicro
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: automatic blot

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 80 K / Max: 90 K / Average: 80 K
Alignment procedureLegacy - Astigmatism: 110
DateJan 2, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 16 / Average electron dose: 20 e/Å2 / Od range: 0.7 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: Phase correction
Final two d classificationNumber classes: 400
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Details: Final map was obtained from 240 best classes / Number images used: 7000

-
Atomic model buiding 1

Initial modelPDB ID:

1tup


Chain - Chain ID: B
SoftwareName: URO
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. other PDB entries used in addition: 1c26 and 1t4f
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Best correlation

+
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