[English] 日本語
Yorodumi
- PDB-4rg2: Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rg2
TitleTudor Domain of Tumor suppressor p53BP1 with small molecule ligand
ComponentsTumor suppressor p53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 Tudor / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / positive regulation of DNA-binding transcription factor activity / double-strand break repair via nonhomologous end joining / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. ...: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
3-bromo-N-[3-(tert-butylamino)propyl]benzamide / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDong, A. / Mader, P. / James, L. / Perfetti, M. / Tempel, W. / Frye, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Chem. Biol. / Year: 2015
Title: Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1.
Authors: Perfetti, M.T. / Baughman, B.M. / Dickson, B.M. / Mu, Y. / Cui, G. / Mader, P. / Dong, A. / Norris, J.L. / Rothbart, S.B. / Strahl, B.D. / Brown, P.J. / Janzen, W.P. / Arrowsmith, C.H. / ...Authors: Perfetti, M.T. / Baughman, B.M. / Dickson, B.M. / Mu, Y. / Cui, G. / Mader, P. / Dong, A. / Norris, J.L. / Rothbart, S.B. / Strahl, B.D. / Brown, P.J. / Janzen, W.P. / Arrowsmith, C.H. / Mer, G. / McBride, K.M. / James, L.I. / Frye, S.V.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.3Sep 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor suppressor p53-binding protein 1
B: Tumor suppressor p53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,74318
Polymers28,2442
Non-polymers49916
Water3,405189
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-2 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.548, 100.458, 83.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1829-

HOH

21A-1840-

HOH

31B-1820-

HOH

-
Components

#1: Protein Tumor suppressor p53-binding protein 1 / 53BP1 / p53-binding protein 1 / p53BP1


Mass: 14121.893 Da / Num. of mol.: 2 / Fragment: Tudor domain (UNP residues 1483-1606)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q12888
#2: Chemical ChemComp-3OO / 3-bromo-N-[3-(tert-butylamino)propyl]benzamide


Mass: 313.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21BrN2O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 19% PEG3350, 0.15 M DL-malic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2014
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 48740 / % possible obs: 98.1 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.049 / Χ2: 0.995 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.535.80.6720400.645182.9
1.53-1.556.50.66821990.655189
1.55-1.586.70.5522650.678193.5
1.58-1.6270.52424010.68198
1.62-1.657.60.45624700.6911100
1.65-1.6980.42624540.7111100
1.69-1.738.10.34524670.7271100
1.73-1.788.20.24624640.7431100
1.78-1.838.20.19924520.7971100
1.83-1.898.20.16224950.8281100
1.89-1.968.20.1224370.8951100
1.96-2.048.20.0924710.9141100
2.04-2.138.20.07224760.9251100
2.13-2.248.20.06124870.9271100
2.24-2.388.20.05524960.9921100
2.38-2.568.10.05624731.2361100
2.56-2.828.10.05825281.7541100
2.82-3.2380.04925001.9721100
3.23-4.077.80.03425451.4321100
4.07-507.50.03126201.278198.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.76 Å25.15 Å
Translation1.76 Å25.15 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
Coot0.7.1model building
GRADEv1.101refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G3R

2g3r


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2238 / WRfactor Rwork: 0.1974 / FOM work R set: 0.795 / SU B: 1.762 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0741 / SU Rfree: 0.0742 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1433 2.9 %RANDOM
Rwork0.1971 ---
obs0.1977 47270 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.88 Å2 / Biso mean: 28.845 Å2 / Biso min: 15 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å2-0 Å2-0 Å2
2--2.93 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 42 189 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192166
X-RAY DIFFRACTIONr_bond_other_d0.0010.022058
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9572930
X-RAY DIFFRACTIONr_angle_other_deg0.73534734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9423.47495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3931514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
X-RAY DIFFRACTIONr_mcbond_it1.7232.7311054
X-RAY DIFFRACTIONr_mcbond_other1.7222.7311055
X-RAY DIFFRACTIONr_mcangle_it2.6744.0791336
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 89 -
Rwork0.295 2934 -
all-3023 -
obs--83.67 %

+
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://pdbjlvh1.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