[English] 日本語
Yorodumi
- PDB-7z71: Crystal structure of p63 DBD in complex with darpin C14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z71
TitleCrystal structure of p63 DBD in complex with darpin C14
Components
  • Darpin C14
  • Isoform 4 of Tumor protein 63
KeywordsDNA BINDING PROTEIN / p63 / TP63 / darpin / 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 / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / positive regulation of keratinocyte proliferation / establishment of planar polarity / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / 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 / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / skin morphogenesis / positive regulation of cell cycle G1/S phase transition / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / 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 / regulation of epidermal cell division / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of stem cell proliferation / epithelial cell development / 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 / negative regulation of cellular senescence / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / positive regulation of apoptotic signaling pathway / stem cell proliferation / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / protein tetramerization / promoter-specific chromatin binding / cellular senescence / p53 binding / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / dendrite / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tumour protein p63, 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) ...Tumour protein p63, 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Death Differ. / Year: 2022
Title: Designed Ankyrin Repeat Proteins as a tool box for analyzing p63.
Authors: Strubel, A. / Munick, P. / Chaikuad, A. / Dreier, B. / Schaefer, J. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Knapp, S. / Pluckthun, A. / Dotsch, V.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 4 of Tumor protein 63
B: Darpin C14
C: Isoform 4 of Tumor protein 63
D: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9026
Polymers78,7714
Non-polymers1312
Water12,394688
1
A: Isoform 4 of Tumor protein 63
B: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4513
Polymers39,3862
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-0 kcal/mol
Surface area16160 Å2
MethodPISA
2
C: Isoform 4 of Tumor protein 63
D: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4513
Polymers39,3862
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-5 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 63.930, 65.504
Angle α, β, γ (deg.)114.460, 94.600, 104.060
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILEAA125 - 3205 - 200
21ALAALAILEILECC125 - 3205 - 200
12ASPASPALAALABB3 - 1593 - 159
22ASPASPALAALADD3 - 1593 - 159

NCS ensembles :
ID
1
2

-
Components

#1: Protein Isoform 4 of 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: 22752.920 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 Darpin C14


Mass: 16632.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.85→44.64 Å / Num. obs: 58153 / % possible obs: 91.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.913.80.119.557680.9750.0840.16192.6
7.17-44.643.60.0249950.9990.0150.02891

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qyn, 6fpb

3qyn

6fpb


Resolution: 1.85→42.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.005 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 2857 4.9 %RANDOM
Rwork0.142 ---
obs0.1439 55294 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.01 Å2 / Biso mean: 27.074 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20.06 Å2-0.2 Å2
2--0.07 Å21.15 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.85→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 2 688 6024
Biso mean--23.93 35.15 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175234
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6437503
X-RAY DIFFRACTIONr_angle_other_deg1.4531.57912104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7523.456272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8041529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021156
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56520.12
12C56520.12
21B48360.08
22D48360.08
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 206 -
Rwork0.147 4159 -
all-4365 -
obs--92.36 %
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)
10.359-0.18580.11340.5202-0.22580.57110.0360.00950.0324-0.0308-0.0232-0.0004-0.0011-0.0448-0.01280.0461-0.0057-0.03380.05410.02560.055722.550925.200936.4866
20.257-0.33710.28950.9456-0.15091.57030.01760.01750.03-0.0117-0.0473-0.1008-0.039800.02970.0258-0.0079-0.03350.03510.02980.067629.411228.41238.844
30.433-0.16990.55040.2402-0.16020.73040.10330.0164-0.0258-0.0843-0.05070.03980.1347-0.0116-0.05270.0504-0.0051-0.04110.06760.03110.061119.098424.316332.2493
43.42891.4426-0.78551.07450.65072.29130.03210.0257-0.27890.01230.0575-0.22-0.04860.1332-0.08960.0282-0.0257-0.0410.03920.03530.138834.073445.224914.7828
50.94370.0576-0.19060.58970.04410.35620.0008-0.0556-0.0039-0.01310.007-0.0365-0.0517-0.0455-0.00780.0275-0.0023-0.03020.04280.03730.070212.881441.815715.9965
65.5074-4.03842.29986.5799-2.26154.3842-0.0085-0.19420.10560.3867-0.0250.1793-0.1498-0.21780.03350.045-0.00020.02870.12650.0380.0641-2.587841.060427.0247
70.3988-0.3380.04271.3952-0.39050.55730.031-0.0280.0291-0.0147-0.0549-0.03830.00970.01680.02390.0284-0.0065-0.030.01530.01420.061312.93543.1613.4715
80.43110.16570.08080.7951-0.31020.2590.0373-0.01070.0297-0.0014-0.01580.01540.0357-0.0218-0.02150.0457-0.0029-0.03140.02850.01740.07558.66061.0522.4679
90.04540.14750.01012.6545-1.0050.52270.020.00310.02040.0424-0.06880.0416-0.00760.06350.04880.033-0.0055-0.01740.03190.0210.116319.29296.7813.8989
104.49760.354-0.21461.04350.10792.55720.0289-0.08070.12360.0049-0.05810.21840.2859-0.33480.02920.0431-0.0417-0.03260.05070.00010.1684-0.775727.0726-4.1448
111.05030.2696-0.17360.6008-0.08180.4148-0.04530.0419-0.0492-0.0721-0.00770.0561-0.01840.02040.0530.0345-0.0161-0.04590.0160.0160.091816.36930.1754-6.1655
121.9093-0.0629-0.22762.04280.31833.147-0.08810.0864-0.1429-0.2534-0.0746-0.26210.00080.49120.16270.04080.00720.02530.09360.04450.12133.965627.6979-10.7929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 211
2X-RAY DIFFRACTION2A212 - 290
3X-RAY DIFFRACTION3A291 - 320
4X-RAY DIFFRACTION4B3 - 26
5X-RAY DIFFRACTION5B27 - 144
6X-RAY DIFFRACTION6B145 - 159
7X-RAY DIFFRACTION7C125 - 219
8X-RAY DIFFRACTION8C220 - 290
9X-RAY DIFFRACTION9C291 - 320
10X-RAY DIFFRACTION10D3 - 26
11X-RAY DIFFRACTION11D27 - 116
12X-RAY DIFFRACTION12D117 - 159

+
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