[English] 日本語
Yorodumi
- PDB-4qo1: p53 DNA binding domain in complex with Nb139 -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / determination of adult lifespan / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / PML body / cellular senescence / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / intracellular protein localization / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process / histone deacetylase binding
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 ...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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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