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- PDB-4qo1: p53 DNA binding domain in complex with Nb139 -

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Basic information

Entry
Database: PDB / ID: 4qo1
Titlep53 DNA binding domain in complex with Nb139
Components
  • Cellular tumor antigen p53P53
  • Nb139 Nanobody against the DNA-binding domain of p53
KeywordsApoptosis / transcription / Immunoglobulin fold / DNA binding
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of neuroblast proliferation / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / neuroblast proliferation / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / chromosome organization / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / embryonic organ development / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / response to salt stress / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation
Similarity search - Function
Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 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 / p53-like transcription factor, DNA-binding / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å
AuthorsDe Gieter, S. / Bethuyne, J. / Gettemans, J. / Garcia-Pino, A. / Loris, R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A nanobody modulates the p53 transcriptional program without perturbing its functional architecture.
Authors: Bethuyne, J. / De Gieter, S. / Zwaenepoel, O. / Garcia-Pino, A. / Durinck, K. / Verhelle, A. / Hassanzadeh-Ghassabeh, G. / Speleman, F. / Loris, R. / Gettemans, J.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nb139 Nanobody against the DNA-binding domain of p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3403
Polymers42,2742
Non-polymers651
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.360, 68.280, 109.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Nb139 Nanobody against the DNA-binding domain of p53


Mass: 16648.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 25626.031 Da / Num. of mol.: 1 / Fragment: p53DBD, unp residues 92-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals of the complex were obtained at 293K using the hanging-drop vapour diffusion method after mixing 1:l protein solution with 1:l reservoir solution equilibrated against 125 ul 0.2 M ...Details: Crystals of the complex were obtained at 293K using the hanging-drop vapour diffusion method after mixing 1:l protein solution with 1:l reservoir solution equilibrated against 125 ul 0.2 M potassium formate 20% w/v PEG 3350 reservoir solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2013
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→42.82 Å / Num. all: 27046 / Num. obs: 27046 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.1033 / Net I/σ(I): 10.34

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MVF

1mvf


Resolution: 1.924→42.823 Å / SU ML: 0.25 / σ(F): 1.38 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1353 5 %Random
Rwork0.1645 ---
obs0.1666 27044 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.924→42.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 1 304 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072558
X-RAY DIFFRACTIONf_angle_d0.9893479
X-RAY DIFFRACTIONf_dihedral_angle_d11.928917
X-RAY DIFFRACTIONf_chiral_restr0.041374
X-RAY DIFFRACTIONf_plane_restr0.005460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9236-1.99240.33471280.29692420X-RAY DIFFRACTION95
1.9924-2.07220.27721320.23832520X-RAY DIFFRACTION100
2.0722-2.16650.24561330.20072525X-RAY DIFFRACTION100
2.1665-2.28070.26691350.18182565X-RAY DIFFRACTION100
2.2807-2.42360.24251340.17862549X-RAY DIFFRACTION100
2.4236-2.61070.2011350.17652565X-RAY DIFFRACTION100
2.6107-2.87330.23531370.172593X-RAY DIFFRACTION100
2.8733-3.2890.19111360.15722584X-RAY DIFFRACTION100
3.289-4.14320.17141380.13222617X-RAY DIFFRACTION100
4.1432-42.83360.16321450.13772753X-RAY DIFFRACTION100
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)
12.7183-0.6816-0.0747.56171.03883.92610.08590.05080.0071-0.62120.0272-0.17040.1717-0.4777-0.05290.4026-0.06030.04880.33790.00610.1744-18.7636.1468-6.071
24.7067-1.4554-0.30042.76123.69285.62710.4041-0.06160.11480.437-0.37830.1233-0.0216-0.22810.03340.32290.00350.03250.2541-0.00730.1829-15.974740.4198-2.6278
38.0403-2.02243.8489.4509-1.11522.1549-0.07020.70730.4162-1.9278-0.169-0.4471-0.60020.12420.24920.5819-0.0360.09940.33820.00760.3852-15.541853.60514.5851
43.4761.79311.78495.37132.02612.16260.1378-0.0289-0.023-0.4778-0.54070.4830.4739-0.61160.32610.3809-0.0996-0.00770.3272-0.04580.1938-21.212139.84445.2304
56.50771.52052.55943.28782.48732.26280.31540.1948-0.50790.3689-0.26810.26811.1092-1.0234-0.03490.6254-0.2680.00010.5359-0.02490.2711-24.997633.30026.0179
63.8030.1281.74486.26953.08373.32360.2702-0.2408-0.31280.35750.0544-0.32861.1890.0848-0.24190.4922-0.0036-0.04690.2368-0.00010.2237-12.137836.47678.8924
77.9031.57041.87763.88112.32629.18960.2831-0.11720.39130.0046-0.171-0.1859-0.14220.7288-0.22940.3807-0.00140.05790.3401-0.01950.243-11.787342.2020.7875
82.9931-0.7873-0.18549.16864.80694.46780.05730.1666-0.39580.0509-0.0099-0.26970.92-0.3721-0.04410.5633-0.11030.03620.3426-0.0490.2849-21.481630.6313-0.74
93.1313-0.11411.04962.63570.15575.95210.2674-0.61230.29210.1983-0.40530.21610.5858-1.45270.09340.2877-0.10710.02390.4264-0.04530.2268-24.40143.835110.7055
105.3362-0.8568-0.18887.19133.74846.6977-0.2669-0.0978-0.3565-0.1943-0.57540.83570.3341-0.84690.76970.6962-0.09990.00670.4331-0.09890.3488-24.534926.1808-11.5123
114.65570.0761-0.32142.09480.72194.88780.12440.2023-0.015-0.3308-0.02920.17590.0915-0.0998-0.09640.1732-0.0059-0.03080.17260.03380.2091-6.929556.099914.7387
120.30410.6949-0.06851.96580.04410.72580.0182-0.0520.05860.1531-0.01040.0541-0.0507-0.0043-0.01480.20140.00910.01780.1788-0.00890.1864-0.513963.183527.985
132.80820.5402-1.31320.3475-0.21412.8698-0.00820.3468-0.03-0.0916-0.026-0.0421-0.0590.00040.02240.20010.0075-0.00450.1345-0.01380.18045.438351.325215.801
145.00171.8368-1.68641.7184-0.88883.99140.0836-0.4886-0.59310.1317-0.141-0.30970.35350.6230.15830.23780.048-0.00030.22280.00950.303911.093743.673529.0357
152.57630.8496-0.23673.7493-0.04225.58050.06840.0938-0.1474-0.06950.0456-0.08050.2626-0.0336-0.09320.10620.0118-00.10360.010.1502-0.75644.377124.7677
165.1454-2.8731-1.31556.39630.74412.529-0.1339-0.29010.30080.88080.0830.451-0.074-0.23880.02960.24730.00350.03970.2022-0.03170.2383-10.384254.931630.5442
171.25030.2240.66271.01640.08671.5301-0.0179-0.00310.10610.0339-0.0265-0.0603-0.0060.06410.04310.16870.00010.01930.144-0.00860.17272.86455.304521.7852
186.9307-3.64311.79337.7921-2.95245.1947-0.10640.40330.4856-0.2918-0.0566-0.6607-0.09890.4440.28070.2159-0.04430.05150.2195-0.02480.283112.432772.699222.2484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 40 )
5X-RAY DIFFRACTION5chain 'A' and (resid 41 through 52 )
6X-RAY DIFFRACTION6chain 'A' and (resid 53 through 74 )
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 84 )
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 99 )
9X-RAY DIFFRACTION9chain 'A' and (resid 100 through 117 )
10X-RAY DIFFRACTION10chain 'A' and (resid 118 through 129 )
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 112 )
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 176 )
14X-RAY DIFFRACTION14chain 'B' and (resid 177 through 194 )
15X-RAY DIFFRACTION15chain 'B' and (resid 195 through 213 )
16X-RAY DIFFRACTION16chain 'B' and (resid 214 through 229 )
17X-RAY DIFFRACTION17chain 'B' and (resid 230 through 277 )
18X-RAY DIFFRACTION18chain 'B' and (resid 278 through 290 )

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