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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 / 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 / Activation of NOXA and translocation to mitochondria / 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 / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress
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)
Voxel sizeX=Y=Z: 3.89969 Å
Density
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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