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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


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / 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 by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
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 / p53 tumour suppressor family ...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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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
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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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