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- PDB-4a63: Crystal structure of the p73-ASPP2 complex at 2.6A resolution -

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Basic information

Entry
Database: PDB / ID: 4a63
TitleCrystal structure of the p73-ASPP2 complex at 2.6A resolution
Components
  • APOPTOSIS STIMULATING OF P53 PROTEIN 2
  • TUMOUR PROTEIN 73
KeywordsCELL CYCLE / TP53BP2 / TUMOUR SUPPRESSOR / ANKYRINS / APOPTOSIS REGULATORY PROTEINS
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis ...positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuron differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / digestive tract morphogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of cell cycle / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of oligodendrocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell size / positive regulation of execution phase of apoptosis / NF-kappaB binding / neuron development / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / release of cytochrome c from mitochondria / transcription corepressor binding / post-embryonic development / hippocampus development / protein tetramerization / kidney development / SH3 domain binding / 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 / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / response to xenobiotic stimulus / DNA-binding transcription factor activity / inflammatory response / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / centrosome / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Tumour protein p73, SAM domain / Immunoglobulin-like - #720 / Ankyrin repeat / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif ...: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Tumour protein p73, SAM domain / Immunoglobulin-like - #720 / Ankyrin repeat / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / Ankyrin repeat-containing domain / 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) / SH3 Domains / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / SH3 domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Roll / Ubiquitin-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Tumor protein p73 / Apoptosis-stimulating of p53 protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsCanning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. ...Canning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Bullock, A.N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis for Aspp2 Recognition by the Tumor Suppressor P73.
Authors: Canning, P. / von Delft, F. / Bullock, A.N.
History
DepositionOct 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references / Structure summary
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOUR PROTEIN 73
B: APOPTOSIS STIMULATING OF P53 PROTEIN 2
C: TUMOUR PROTEIN 73
D: APOPTOSIS STIMULATING OF P53 PROTEIN 2
E: TUMOUR PROTEIN 73
F: APOPTOSIS STIMULATING OF P53 PROTEIN 2
G: TUMOUR PROTEIN 73
H: APOPTOSIS STIMULATING OF P53 PROTEIN 2
I: TUMOUR PROTEIN 73
J: APOPTOSIS STIMULATING OF P53 PROTEIN 2
K: TUMOUR PROTEIN 73
L: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,62326
Polymers301,76412
Non-polymers85814
Water12,088671
1
A: TUMOUR PROTEIN 73
B: APOPTOSIS STIMULATING OF P53 PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)50,2942
Polymers50,2942
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-4.4 kcal/mol
Surface area23880 Å2
MethodPISA
2
C: TUMOUR PROTEIN 73
D: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5376
Polymers50,2942
Non-polymers2434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-4.6 kcal/mol
Surface area22920 Å2
MethodPISA
3
E: TUMOUR PROTEIN 73
F: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3593
Polymers50,2942
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-5.9 kcal/mol
Surface area22730 Å2
MethodPISA
4
G: TUMOUR PROTEIN 73
H: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4184
Polymers50,2942
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-3.8 kcal/mol
Surface area23070 Å2
MethodPISA
5
I: TUMOUR PROTEIN 73
J: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4785
Polymers50,2942
Non-polymers1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-4.1 kcal/mol
Surface area23610 Å2
MethodPISA
6
K: TUMOUR PROTEIN 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5264
Polymers23,3431
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
L: APOPTOSIS STIMULATING OF P53 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0112
Polymers26,9511
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.810, 170.100, 177.555
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9978, -0.0418, 0.0521), (-0.0385, 0.9973, 0.0625), (-0.0546, 0.0603, -0.9967)118.5932, 2.6553, 125.0005
2given(0.9982, -0.0509, -0.0313), (0.0511, 0.9987, 0.0065), (0.0309, -0.0081, 0.9995)-4.9379, -1.0056, 59.6942
3given(0.9999, 0.003, 0.0127), (0.0033, -0.9997, -0.0239), (0.0126, 0.024, -0.9996)-66.4735, 46.3594, 117.1661
4given(-0.9985, 0.0258, -0.0487), (-0.0278, -0.9988, 0.0406), (-0.0476, 0.0419, 0.998)56.5417, 44.506, 1.6732
5given(-0.999, 0.0263, -0.0351), (-0.0272, -0.9993, 0.0246), (-0.0344, 0.0255, 0.9991)59.9801, 46.566, 60.174
6given(-0.9998, 0.0167, -0.0114), (-0.0179, -0.993, 0.1164), (-0.0094, 0.1166, 0.9931)54.2497, 38.9586, -3.2515
7given(-0.9982, -0.0583, 0.0118), (-0.0589, 0.9963, -0.0626), (-0.0081, -0.0632, -0.998)-12.1315, 3.1359, 118.5837
8given(-0.9997, 0.0253, -0.0034), (-0.0254, -0.9995, 0.021), (-0.0028, 0.0211, 0.9998)59.4735, 46.6306, 58.421
9given(0.9993, -0.0384, -0.0033), (0.0385, 0.9977, 0.0553), (0.0012, -0.0554, 0.9985)-5.3151, -0.8583, 59.9342
10given(0.9994, 0.0344, -0.0027), (0.0344, -0.9994, 0.007), (-0.0025, -0.0071, -1)-67.0543, 42.5625, 119.1191

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Components

#1: Protein
TUMOUR PROTEIN 73 / P53-LIKE TRANSCRIPTION FACTOR / P53-RELATED PROTEIN


Mass: 23342.561 Da / Num. of mol.: 6 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: O15350
#2: Protein
APOPTOSIS STIMULATING OF P53 PROTEIN 2 / BCL2-BINDING PROTEIN / BBP / RENAL CARCINOMA ANTIGEN NY-REN-51 / TUMOR SUPPRESSOR P53-BINDING ...BCL2-BINDING PROTEIN / BBP / RENAL CARCINOMA ANTIGEN NY-REN-51 / TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 / 53BP2 / P53-BINDING PROTEIN 2 / P53BP2


Mass: 26951.475 Da / Num. of mol.: 6 / Fragment: ANKYRIN AND SH3 DOMAINS, RESIDUES 892-1128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q13625
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsACETATE (ACT): PRESENT IN CRYSTALLIZATION BUFFER

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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: 3.32 Å3/Da / Density % sol: 63.03 % / Description: NONE
Crystal growDetails: 1.00M NA/KPO4, 0.1M ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→88.72 Å / Num. obs: 111026 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 43.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2XWC AND 1YCS CHAIN B

2xwc

1ycs


Resolution: 2.27→85.05 Å / Cor.coef. Fo:Fc: 0.7815 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.184
Details: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING ...Details: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING PSEUDO TRANSLATIONAL SYMMETRY. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19288. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0 NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 8824 5.02 %RANDOM
Rwork0.2151 ---
obs0.2166 175926 97.07 %-
Displacement parametersBiso mean: 51.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.0135 Å20 Å2-2.2847 Å2
2---6.4261 Å20 Å2
3---7.4395 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.27→85.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18374 0 41 671 19086
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118918HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0825841HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8430SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes466HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2792HARMONIC5
X-RAY DIFFRACTIONt_it18918HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2517SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21358SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2617 693 5.29 %
Rwork0.2422 12399 -
all0.2432 13092 -
obs--97.07 %

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