[English] 日本語
Yorodumi
- EMDB-22827: P53 tetramer from Glioblastoma -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22827
TitleP53 tetramer from Glioblastoma
Map dataP53 tetramer from Glioblastoma
Sample
  • Complex: Tetramer of p53 and DNA
    • Protein or peptide: Tumor suppressor protein, P53
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsSolares MJ / Kelly DF
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA193578 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA219700 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA227261 United States
CitationJournal: Anal Chem / Year: 2020
Title: Microchip-Based Structure Determination of Disease-Relevant p53.
Authors: Maria J Solares / G M Jonaid / William Y Luqiu / Yanping Liang / Madison C Evans / William J Dearnaley / Zhi Sheng / Deborah F Kelly /
Abstract: The tumor suppressor protein TP53 (p53) plays a multifaceted role in all cells of the human body. Mutations in the gene are often involved in cancer induction and disease progression. Despite its ...The tumor suppressor protein TP53 (p53) plays a multifaceted role in all cells of the human body. Mutations in the gene are often involved in cancer induction and disease progression. Despite its important role in health and development, structural information for p53 remains incomplete. Here, we present a microchip-based technology to facilitate structural studies of p53 assemblies derived from human cancer cells. These devices do not introduce foreign sequences to the gene and maintain naturally occurring post-translational modifications. Using cryo-electron microscopy, structures for the p53 monomer (∼50 kDa) and tetramer (∼200 kDa) were resolved to ∼4.8 and ∼7 Å, respectively. These structures revealed new insights for flexible regions of p53 along with biologically relevant ubiquitination sites. Collectively, the convergence of nanotechnology tools and structural imaging builds a strong framework to understand the oncogenic impact of p53 in human tissues.
History
DepositionOct 9, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0116
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0116
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22827.png

Downloads & links

-
Map

FileDownload / File: emd_22827.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP53 tetramer from Glioblastoma
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 200 pix.
= 200. Å		1 Å/pix.
x 200 pix.
= 200. Å		1 Å/pix.
x 200 pix.
= 200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0116 / Movie #1: 0.0116
Minimum - Maximum-0.009583039 - 0.017134355
Average (Standard dev.)0.0016868218 (±0.0028828138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 200.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z200.000200.000200.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0100.0170.002

-
Supplemental data

-
Sample components

-
Entire : Tetramer of p53 and DNA

EntireName: Tetramer of p53 and DNA
Components
  • Complex: Tetramer of p53 and DNA
    • Protein or peptide: Tumor suppressor protein, P53

-
Supramolecule #1: Tetramer of p53 and DNA

SupramoleculeName: Tetramer of p53 and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: isolated from glioblastoma cells
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: epithelial / Location in cell: nucleus
Molecular weightTheoretical: 200 KDa

-
Macromolecule #1: Tumor suppressor protein, P53

MacromoleculeName: Tumor suppressor protein, P53 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: epithelial
SequenceString: MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEA APPVAPAPAA PTPAAPAPAP SWPLSSSVPS QKTYQGSYGF RLGFLHSGTA K SVTCTYSP ALNKMFCQLA KTCPVQLWVD STPPPGTRVR AMAIYKQSQH ...String:
MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEA APPVAPAPAA PTPAAPAPAP SWPLSSSVPS QKTYQGSYGF RLGFLHSGTA K SVTCTYSP ALNKMFCQLA KTCPVQLWVD STPPPGTRVR AMAIYKQSQH MTEVVRRCPH HE RCSDSDG LAPPQHLIRV EGNLRVEYLD DRNTFRHSVV VPYEPPEVGS DCTTIHYNYM CNS SCMGGM NRRPILTIIT LEDSSGNLLG RNSFEVRVCA CPGRDRRTEE ENLRKKGEPH HELP PGSTK RALPNNTSSS PQPKKKPLDG EYFTLQIRGR ERFEMFRELN EALELKDAQA GKEPG GSRA HSSHLKSKKG QSTSRHKKLM FKTEGPDSD

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.2
Details: 20 mM HEPES, (pH 7.2), 140 mM NaCl, 2 mM CaCl2, 2 mM MgCl2, and 5 mM imidazole
GridMaterial: SILICON NITRIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III / Details: blotted for 6 seconds before plunging.
DetailsConcentrated onto 25% Ni-NTA coating on silicon nitride microchips

-
Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 2 / Number real images: 150 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 92000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 9558
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ac0

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 9558
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3)

-
Atomic model buiding 1

Initial modelPDB ID:

2ac0

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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