[English] 日本語
Yorodumi
- PDB-8p9d: Crystal structure of p63-p73 heterotetramer (tetramerisation doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p9d
TitleCrystal structure of p63-p73 heterotetramer (tetramerisation domain) in complex with darpin 1810 A2
Components
  • Darpin 1810 A2
  • Tumor protein 63
  • Tumor protein p73
KeywordsDNA BINDING PROTEIN / p63 / p73 / tetramerization domain / darpin / heterotetramer / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / positive regulation of lung ciliated cell differentiation / negative regulation of mesoderm development / prostatic bud formation / cerebrospinal fluid secretion / female genitalia morphogenesis / positive regulation of keratinocyte proliferation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / positive regulation of lung ciliated cell differentiation / negative regulation of mesoderm development / prostatic bud formation / cerebrospinal fluid secretion / female genitalia morphogenesis / positive regulation of keratinocyte proliferation / establishment of planar polarity / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / negative regulation of keratinocyte differentiation / polarized epithelial cell differentiation / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / negative regulation of cardiac muscle cell proliferation / skin morphogenesis / positive regulation of cell cycle G1/S phase transition / negative regulation of intracellular estrogen receptor signaling pathway / sympathetic nervous system development / cranial skeletal system development / post-anal tail morphogenesis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / embryonic forelimb morphogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / embryonic hindlimb morphogenesis / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / WW domain binding / epithelial cell development / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis / positive regulation of Notch signaling pathway / regulation of epidermal cell division / positive regulation of stem cell proliferation / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / negative regulation of cellular senescence / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell size / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / neuron development / mismatch repair / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / release of cytochrome c from mitochondria / positive regulation of apoptotic signaling pathway / transcription corepressor binding / stem cell proliferation / post-embryonic development / skeletal system development / determination of adult lifespan / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / protein tetramerization / kidney development / promoter-specific chromatin binding / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cellular senescence / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / neuron apoptotic process / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of MAPK cascade / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / response to xenobiotic stimulus / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / apoptotic process / dendrite / DNA damage response / centrosome
Similarity search - Function
Tumour protein p63, SAM domain / Tumour protein p73, SAM domain / 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 ...Tumour protein p63, SAM domain / Tumour protein p73, SAM domain / 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 / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Tumor protein p73 / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Death Dis / Year: 2023
Title: DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma.
Authors: Strubel, A. / Munick, P. / Hartmann, O. / Chaikuad, A. / Dreier, B. / Schaefer, J.V. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Buck, V. / Rosenfeldt, M. / Knapp, S. / ...Authors: Strubel, A. / Munick, P. / Hartmann, O. / Chaikuad, A. / Dreier, B. / Schaefer, J.V. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Buck, V. / Rosenfeldt, M. / Knapp, S. / Pluckthun, A. / Diefenbacher, M.E. / Dotsch, V.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly
Item: _citation.journal_id_ISSN / _entity.pdbx_description ..._citation.journal_id_ISSN / _entity.pdbx_description / _entity.src_method / _pdbx_struct_assembly.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor protein 63
B: Tumor protein p73
C: Tumor protein 63
D: Tumor protein p73
E: Darpin 1810 A2
F: Darpin 1810 A2


Theoretical massNumber of molelcules
Total (without water)53,2786
Polymers53,2786
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-87 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.729, 113.186, 135.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Tumor protein 63 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / ...p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p40 / p51


Mass: 7380.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP63, KET, P63, P73H, P73L, TP73L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3D4
#2: Protein/peptide Tumor protein p73 / p53-like transcription factor / p53-related protein


Mass: 6034.894 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP73, P73 / Production host: Escherichia coli (E. coli) / References: UniProt: O15350
#3: Protein Darpin 1810 A2


Mass: 13223.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.1M bis-tris propane pH 7.0, 0.2M salicylic, sodium salt

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.08 Å / Num. obs: 17853 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 1.01 / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2 / Num. unique obs: 2555 / CC1/2: 0.751 / Rpim(I) all: 0.393 / Rrim(I) all: 1.01 / Χ2: 1.05

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 38.382 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25164 906 5.1 %RANDOM
Rwork0.21466 ---
obs0.21656 16896 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.644 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å2-0 Å20 Å2
2--5.12 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 6 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133510
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173299
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.6324751
X-RAY DIFFRACTIONr_angle_other_deg1.1191.5787678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1225.026193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06215640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7931514
X-RAY DIFFRACTIONr_chiral_restr0.0470.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023914
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.524.8811738
X-RAY DIFFRACTIONr_mcbond_other2.5194.881737
X-RAY DIFFRACTIONr_mcangle_it3.9577.312162
X-RAY DIFFRACTIONr_mcangle_other3.9577.3112163
X-RAY DIFFRACTIONr_scbond_it2.895.2231772
X-RAY DIFFRACTIONr_scbond_other2.8855.2231772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6377.6952589
X-RAY DIFFRACTIONr_long_range_B_refined6.4357.0643783
X-RAY DIFFRACTIONr_long_range_B_other6.4357.0743784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A12610.14
12C12610.14
21B12600.13
22D12600.13
31E37790.08
32F37790.08
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 68 -
Rwork0.377 1230 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.51450.99674.63664.6907-0.53368.71740.0784-0.5176-0.36170.2468-0.16510.0662-0.0898-0.19770.08670.29570.06990.10620.22570.01230.11611.196612.4851-0.0911
23.44470.0394-4.19521.5678-1.508211.81150.2687-0.5343-0.46410.271-0.1471-0.1660.23910.4326-0.12160.3765-0.0072-0.1380.37540.02990.333811.11796.3207-0.1099
34.48252.2672-0.67316.0207-3.06148.54320.03040.1087-0.4108-0.7353-0.1454-0.11770.24710.08870.11510.25550.05840.00910.2960.06660.171314.5539.208814.7828
43.03391.53040.66523.43523.60689.6194-0.17880.2186-0.3126-0.45620.10240.24730.3228-0.28760.07640.22670.0427-0.05310.30820.13050.21099.23157.536114.6257
55.7192-3.4982-0.13387.67960.59642.56370.08360.5991-0.0732-0.22650.0804-0.1066-0.27190.1201-0.16410.0347-0.02180.02150.2822-0.06640.023916.742916.5348-23.4808
69.302-1.6713-0.84524.8891-0.5733.74040.1694-0.96140.14240.3017-0.09530.0599-0.1871-0.001-0.07410.0568-0.02030.0030.32860.08230.059617.334812.790238.9618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 404
2X-RAY DIFFRACTION2B350 - 397
3X-RAY DIFFRACTION3C359 - 404
4X-RAY DIFFRACTION4D352 - 397
5X-RAY DIFFRACTION5E2 - 126
6X-RAY DIFFRACTION6F2 - 126

+
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