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- PDB-9glq: Crystal structure of p73 tetramerisation domain in complex with d... -

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Basic information

Entry
Database: PDB / ID: 9glq
TitleCrystal structure of p73 tetramerisation domain in complex with darpins 1800
Components
  • Darpins 1800
  • Tumor protein p73
KeywordsDNA BINDING PROTEIN / TP73 / tetramerisation domain / darpins / Structural Genomics / Structural Genomics Consortium / SGC
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
: / Tumor protein p73
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionAug 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor protein p73
B: Tumor protein p73
C: Darpins 1800
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4955
Polymers25,3443
Non-polymers1512
Water88349
1
A: Tumor protein p73
B: Tumor protein p73
C: Darpins 1800
hetero molecules

A: Tumor protein p73
B: Tumor protein p73
C: Darpins 1800
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98910
Polymers50,6876
Non-polymers3024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area13350 Å2
ΔGint-106 kcal/mol
Surface area19980 Å2
Unit cell
Length a, b, c (Å)62.763, 94.816, 96.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: 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
#2: Protein Darpins 1800


Mass: 13273.813 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000MME, 0.15M potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.1→48.22 Å / Num. obs: 17152 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Χ2: 1.01 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 2 / Num. unique obs: 1653 / CC1/2: 0.938 / Rpim(I) all: 0.375 / Rrim(I) all: 1.056 / Χ2: 1.08

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.458 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24782 799 4.7 %RANDOM
Rwork0.20224 ---
obs0.2043 16349 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.216 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0 Å2
2--3.93 Å20 Å2
3----3.27 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 7 49 1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131728
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171621
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.6312333
X-RAY DIFFRACTIONr_angle_other_deg1.2431.5783769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25224.89192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08515311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.501157
X-RAY DIFFRACTIONr_chiral_restr0.0580.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
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_it1.8954.247861
X-RAY DIFFRACTIONr_mcbond_other1.8934.245860
X-RAY DIFFRACTIONr_mcangle_it2.9936.3441071
X-RAY DIFFRACTIONr_mcangle_other2.9926.3471072
X-RAY DIFFRACTIONr_scbond_it2.8034.686867
X-RAY DIFFRACTIONr_scbond_other2.8014.691868
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0996.8861263
X-RAY DIFFRACTIONr_long_range_B_refined6.5750.8351928
X-RAY DIFFRACTIONr_long_range_B_other6.5650.6661919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 67 -
Rwork0.288 1183 -
obs--99.92 %
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)
10.8057-0.0795-0.41420.76460.08941.4532-0.185-0.07070.16430.01110.1014-0.07570.16570.19250.08360.27760.0377-0.00210.19840.0010.06476.367427.407644.1971
23.56370.351-0.41760.38170.54914.1496-0.35980.1326-0.036-0.09040.2046-0.01870.53530.36150.15520.30580.03640.03370.1652-0.00530.0126.932923.921146.3179
31.3662-0.5056-1.92550.78321.22846.7538-0.2769-0.1319-0.04110.12720.1444-0.04980.6890.33460.13250.28620.11570.07830.12540.03690.058821.898511.880927.636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A352 - 397
2X-RAY DIFFRACTION2B353 - 396
3X-RAY DIFFRACTION3C1 - 126

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