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- EMDB-0378: p53 dimer assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-0378
Titlep53 dimer assembly
Map datap53 dimer assembly
Sample
  • Complex: p53 dimer assembly
    • Protein or peptide: p53
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsKelly DF / Dearnaley WJ / Varano AC
CitationJournal: Small / Year: 2019
Title: Cryo-EM-On-a-Chip: Custom-Designed Substrates for the 3D Analysis of Macromolecules.
Authors: Nick A Alden / A Cameron Varano / William J Dearnaley / Maria J Solares / William Y Luqiu / Yanping Liang / Zhi Sheng / Sarah M McDonald / John Damiano / Jennifer McConnell / Madeline J ...Authors: Nick A Alden / A Cameron Varano / William J Dearnaley / Maria J Solares / William Y Luqiu / Yanping Liang / Zhi Sheng / Sarah M McDonald / John Damiano / Jennifer McConnell / Madeline J Dukes / Deborah F Kelly /
Abstract: The fight against human disease requires a multidisciplinary scientific approach. Applying tools from seemingly unrelated areas, such as materials science and molecular biology, researchers can ...The fight against human disease requires a multidisciplinary scientific approach. Applying tools from seemingly unrelated areas, such as materials science and molecular biology, researchers can overcome long-standing challenges to improve knowledge of molecular pathologies. Here, custom-designed substrates composed of silicon nitride (SiN) are used to study the 3D attributes of tumor suppressor proteins that function in DNA repair events. New on-chip preparation strategies enable the isolation of native protein complexes from human cancer cells. Combined techniques of cryo-electron microscopy (EM) and molecular modeling reveal a new modified form of the p53 tumor suppressor present in aggressive glioblastoma multiforme cancer cells. Taken together, the findings provide a radical new design for cryo-EM substrates to evaluate the structures of disease-related macromolecules.
History
DepositionDec 3, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseApr 24, 2019-
UpdateJun 5, 2019-
Current statusJun 5, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.569
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.569
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0378.png

Downloads & links

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Map

FileDownload / File: emd_0378.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp53 dimer assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 100 pix.
= 420. Å		4.2 Å/pix.
x 100 pix.
= 420. Å		4.2 Å/pix.
x 100 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.569 / Movie #1: 0.569
Minimum - Maximum-0.55717945 - 1.3238852
Average (Standard dev.)0.0038478214 (±0.03233218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.5571.3240.004

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Supplemental data

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Sample components

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Entire : p53 dimer assembly

EntireName: p53 dimer assembly
Components
  • Complex: p53 dimer assembly
    • Protein or peptide: p53

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Supramolecule #1: p53 dimer assembly

SupramoleculeName: p53 dimer assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Glioblastoma
Molecular weightTheoretical: 116 KDa

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Macromolecule #1: p53

MacromoleculeName: p53 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Organ: Brain / Tissue: Glioblastoma
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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.2 / Component - Name: HEPES buffer
Details: 20 mM HEPES, pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2, 60 mM Imidazole
GridMaterial: SILICON NITRIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III
Details: Blot for 6-10 seconds before plunging, dwell time was 1 second, grid platform was SiN chip..

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 30.0 µm / Number grids imaged: 1 / Number real images: 100 / Average electron dose: 5.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 68000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12144
CTF correctionSoftware - Name: RELION (ver. 2.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ac0


Details: Resolution filtered to ~50 Angstrom
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 12144
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1) / Details: Empirical Bayesian approach
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1) / Details: Empirical Bayesian approach
Final 3D classificationNumber classes: 1 / Avg.num./class: 12144 / Software - Name: RELION (ver. 2.1)

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Atomic model buiding 1

Initial modelPDB ID:

2ac0

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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