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- PDB-9gnb: Structure of p73 SAM domain in complex with DARPin B9 -

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Basic information

Entry
Database: PDB / ID: 9gnb
TitleStructure of p73 SAM domain in complex with DARPin B9
Components
  • Darpin B9
  • Tumor protein p73
KeywordsTRANSCRIPTION / TP73 / DARPin / Tumor suppressor / cancer / transcription factor
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / regulation of cell cycle / ciliary basal body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / centrosome / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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) ...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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMuenick, P. / Strubel, A. / Gebel, J. / Schroeder, M. / Knapp, S.
Funding support Germany, Canada, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
The Structural Genomics Consortium (SGC) Canada
CitationJournal: Cell Death Dis / Year: 2024
Title: DARPins as a novel tool to detect and degrade p73.
Authors: Munick, P. / Zielinski, J. / Strubel, A. / Gutfreund, N. / Dreier, B. / Schaefer, J.V. / Schafer, B. / Gebel, J. / Osterburg, C. / Chaikuad, A. / Knapp, S. / Pluckthun, A. / Dotsch, V.
History
DepositionSep 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein p73
B: Darpin B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1313
Polymers24,0352
Non-polymers961
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-25 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)48.304, 31.234, 68.355
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor protein p73 / p53-like transcription factor / p53-related protein


Mass: 7178.164 Da / Num. of mol.: 1
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
#2: Protein Darpin B9


Mass: 16856.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% PEG6000, 0.1M bicine pH 9.0

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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: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→67.984 Å / Num. obs: 18890 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-67.9860.02418310.0150.02899.7
1.8-1.846.80.34211280.9420.2120.40399.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→67.984 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.308 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2335 968 5.127 %
Rwork0.2012 17912 -
all0.203 --
obs-18880 98.231 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å20 Å2-2.082 Å2
2--1.291 Å20 Å2
3----0.804 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 5 70 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161602
X-RAY DIFFRACTIONr_angle_refined_deg1.581.622281
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5823685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1125.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.888154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined0.2190.2391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21443
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2822
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.214
X-RAY DIFFRACTIONr_nbd_other0.1910.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.26
X-RAY DIFFRACTIONr_mcbond_it2.6953.173865
X-RAY DIFFRACTIONr_mcbond_other2.6773.171864
X-RAY DIFFRACTIONr_mcangle_it3.694.7381076
X-RAY DIFFRACTIONr_mcangle_other3.6964.7411077
X-RAY DIFFRACTIONr_scbond_it3.5353.602814
X-RAY DIFFRACTIONr_scbond_other3.5083.601811
X-RAY DIFFRACTIONr_scangle_it5.3485.2451205
X-RAY DIFFRACTIONr_scangle_other5.3375.2431200
X-RAY DIFFRACTIONr_lrange_it6.75439.4141845
X-RAY DIFFRACTIONr_lrange_other6.74839.3841839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.279780.2513250.25214140.8250.8499.22210.232
1.847-1.8970.302520.24212720.24413430.840.86298.58530.218
1.897-1.9520.329700.23612490.24113560.8560.87797.27140.214
1.952-2.0120.258570.21411840.21612690.9080.91797.79350.197
2.012-2.0780.238670.21311850.21412810.9060.91997.73610.196
2.078-2.1510.269470.20310910.20611940.9090.92595.30990.187
2.151-2.2320.29610.19611040.20111670.9110.93599.82860.181
2.232-2.3230.304530.21110830.21511400.8910.92799.64910.194
2.323-2.4260.257610.21110180.21410920.8980.92698.80950.195
2.426-2.5450.252550.2279680.22910360.9080.90898.74520.217
2.545-2.6820.263520.2019260.2059920.9070.92798.58870.197
2.682-2.8440.345500.2198900.2259600.8880.91697.91670.214
2.844-3.040.221400.2057940.2068720.9280.93995.64220.206
3.04-3.2840.279400.2037740.2068200.9150.93999.26830.206
3.284-3.5960.183440.1947290.1937730.9520.9541000.201
3.596-4.0190.158400.1786520.1776930.9690.96299.85570.189
4.019-4.6380.21310.1815860.1836200.9560.96299.51610.198
4.638-5.6740.207260.1914700.1925240.9540.96194.65650.21
5.674-7.9970.208300.2033800.2044200.9490.95597.6190.227
7.997-67.9840.188140.1732320.1742460.9690.9661000.2

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