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- EMDB-11858: Recombinant human p53, tetrameric state -

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Basic information

Entry
Database: EMDB / ID: EMD-11858
TitleRecombinant human p53, tetrameric state
Map data
Sample
  • Organelle or cellular component: NT*-p53
    • Protein or peptide: NT*-p53
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / mRNA 3'-UTR binding / Regulation of NF-kappa B signaling / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / intracellular protein localization / positive regulation of reactive oxygen species metabolic process / histone deacetylase binding
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 12.8 Å
AuthorsZhong X / Chen G / Kaldmae M / Koeck PJB / Lane DP / Landreh M / Johansson J
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2019-01961 Sweden
CitationJournal: Structure / Year: 2022
Title: A "spindle and thread" mechanism unblocks p53 translation by modulating N-terminal disorder.
Authors: Margit Kaldmäe / Thibault Vosselman / Xueying Zhong / Dilraj Lama / Gefei Chen / Mihkel Saluri / Nina Kronqvist / Jia Wei Siau / Aik Seng Ng / Farid J Ghadessy / Pierre Sabatier / Borivoj ...Authors: Margit Kaldmäe / Thibault Vosselman / Xueying Zhong / Dilraj Lama / Gefei Chen / Mihkel Saluri / Nina Kronqvist / Jia Wei Siau / Aik Seng Ng / Farid J Ghadessy / Pierre Sabatier / Borivoj Vojtesek / Médoune Sarr / Cagla Sahin / Nicklas Österlund / Leopold L Ilag / Venla A Väänänen / Saikiran Sedimbi / Marie Arsenian-Henriksson / Roman A Zubarev / Lennart Nilsson / Philip J B Koeck / Anna Rising / Axel Abelein / Nicolas Fritz / Jan Johansson / David P Lane / Michael Landreh /
Abstract: Disordered proteins pose a major challenge to structural biology. A prominent example is the tumor suppressor p53, whose low expression levels and poor conformational stability hamper the development ...Disordered proteins pose a major challenge to structural biology. A prominent example is the tumor suppressor p53, whose low expression levels and poor conformational stability hamper the development of cancer therapeutics. All these characteristics make it a prime example of "life on the edge of solubility." Here, we investigate whether these features can be modulated by fusing the protein to a highly soluble spider silk domain (NT). The chimeric protein displays highly efficient translation and is fully active in human cancer cells. Biophysical characterization reveals a compact conformation, with the disordered transactivation domain of p53 wrapped around the NT domain. We conclude that interactions with NT help to unblock translation of the proline-rich disordered region of p53. Expression of partially disordered cancer targets is similarly enhanced by NT. In summary, we demonstrate that inducing co-translational folding via a molecular "spindle and thread" mechanism unblocks protein translation in vitro.
History
DepositionOct 19, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11858.png

Downloads & links

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Map

FileDownload / File: emd_11858.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.9 Å/pix.
x 84 pix.
= 327.574 Å		3.9 Å/pix.
x 84 pix.
= 327.574 Å		3.9 Å/pix.
x 84 pix.
= 327.574 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.89969 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.49538314 - 2.1815689
Average (Standard dev.)0.016010623 (±0.14130303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 327.57407 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.89969047619053.89969047619053.8996904761905
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z327.574327.574327.574
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-42-42-42
NC/NR/NS848484
D min/max/mean-0.4952.1820.016

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Supplemental data

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Half map: #2

Fileemd_11858_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11858_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NT*-p53

EntireName: NT*-p53
Components
  • Organelle or cellular component: NT*-p53
    • Protein or peptide: NT*-p53

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Supramolecule #1: NT*-p53

SupramoleculeName: NT*-p53 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 237 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: NT*-p53

MacromoleculeName: NT*-p53 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGHHHHHHSH TTPWTNPGLA ENFMNSFMQG LSSMPGFTAS QLDKMSTIAQ SMVQSIQSLA AQGRTSPNDL QALNMAFASS MAEIAASEEG GGSLSTKTSS IASAMSNAFL QTTGVVNQPF INEITQLVSM FAQAGMNDVS AENLYFQSME EPQSDPSVEP PLSQETFSDL ...String:
MGHHHHHHSH TTPWTNPGLA ENFMNSFMQG LSSMPGFTAS QLDKMSTIAQ SMVQSIQSLA AQGRTSPNDL QALNMAFASS MAEIAASEEG GGSLSTKTSS IASAMSNAFL QTTGVVNQPF INEITQLVSM FAQAGMNDVS AENLYFQSME EPQSDPSVEP PLSQETFSDL WKLLPENNVL SPLPSQAMDD LMLSPDDIEQ WFTEDPGPDE APRMPEAAPP VAPAPAAPTP AAPAPAPSWP LSSSVPSQKT YQGSYGFRLG FLHSGTAKSV TCTYSPALNK MFCQLAKTCP VQLWVDSTPP PGTRVRAMAI YKQSQHMTEV VRRCPHHERC SDSDGLAPPQ HLIRVEGNLR VEYLDDRNTF RHSVVVPYEP PEVGSDCTTI HYNYMCNSSC MGGMNRRPIL TIITLEDSSG NLLGRNSFEV RVCACPGRDR RTEEENLRKK GEPHHELPPG STKRALPNNT SSSPQPKKKP LDGEYFTLQI RGRERFEMFR ELNEALELKD AQAGKEPGGS RAHSSHLKSK KGQSTSRHKK LMFKTEGPDS D

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Acetate 2% (w/v)

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 6519
CTF correctionSoftware - Name: EMAN2 (ver. 2.3)
Software - details: EMAN2 e2ctf_auto.py was used to apply the CTF correction.
Final reconstructionNumber classes used: 32 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6519
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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