[English] 日本語
Yorodumi
- PDB-8t2d: Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t2d
TitleUbiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain
Components
  • Tumor protein p53 binding protein 1
  • Ubiquitin variant i53
KeywordsPROTEIN BINDING / inhibitor
Function / homology
Function and homology information


DNA damage checkpoint signaling / modification-dependent protein catabolic process / protein tag activity / histone binding / nuclear body / protein ubiquitination / ubiquitin protein ligase binding / 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 / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ribosomal protein L2, domain 2 / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tumor protein p53 binding protein 1 / Ubiquitin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsPartridge, J.R. / Holden, J.K. / Wibowo, A.S. / Mulichak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.
Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. ...Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. / Krassovsky, K. / Lalisan, C.D. / Lord, D. / Quejarro, B.J. / Sales-Lee, J. / Shah, M. / Silva, B.J. / Skowronski, J. / Strukov, Y.G. / Thomas, J. / Veraz, M. / Vijay, T. / Wallace, K.A. / Yuan, Y. / Grogan, J.L. / Wienert, B. / Lahiri, P. / Treusch, S. / Dever, D.P. / Soros, V.B. / Partridge, J.R. / Seim, K.L.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ubiquitin variant i53
A: Tumor protein p53 binding protein 1


Theoretical massNumber of molelcules
Total (without water)22,7112
Polymers22,7112
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.511, 46.855, 91.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin variant i53


Mass: 8794.099 Da / Num. of mol.: 1 / Mutation: T12Y, T14E, L67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39
#2: Protein Tumor protein p53 binding protein 1


Mass: 13916.683 Da / Num. of mol.: 1 / Fragment: Tudor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NNK5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.751→29.85 Å / Num. obs: 17557 / % possible obs: 98.89 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06022 / Rpim(I) all: 0.02474 / Rrim(I) all: 0.0653 / Net I/σ(I): 12.41
Reflection shellResolution: 1.751→1.813 Å / Redundancy: 3.8 % / Num. unique obs: 1636 / CC1/2: 0.386 / Rpim(I) all: 0.9374 / % possible all: 94.24

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→29.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.124 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2725 843 4.818 %
Rwork0.2224 16654 -
all0.225 --
obs-17497 98.915 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.232 Å20 Å2-0 Å2
2---0.488 Å20 Å2
3---0.255 Å2
Refinement stepCycle: LAST / Resolution: 1.751→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 38 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161521
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6492096
X-RAY DIFFRACTIONr_angle_other_deg0.4521.5783513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.676512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26610299
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7091073
X-RAY DIFFRACTIONr_chiral_restr0.0640.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_nbd_refined0.2170.2251
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21424
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2729
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.276
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.214
X-RAY DIFFRACTIONr_nbd_other0.230.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.22
X-RAY DIFFRACTIONr_mcbond_it2.933.066757
X-RAY DIFFRACTIONr_mcbond_other2.9293.06756
X-RAY DIFFRACTIONr_mcangle_it4.255.476941
X-RAY DIFFRACTIONr_mcangle_other4.2565.48942
X-RAY DIFFRACTIONr_scbond_it3.8363.585804
X-RAY DIFFRACTIONr_scbond_other3.8373.584804
X-RAY DIFFRACTIONr_scangle_it6.0246.3681155
X-RAY DIFFRACTIONr_scangle_other6.0216.3711156
X-RAY DIFFRACTIONr_lrange_it7.84133.921694
X-RAY DIFFRACTIONr_lrange_other7.84433.941692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.751-1.7960.407550.36511690.36613070.8810.88993.64960.368
1.796-1.8450.327500.3411310.33912170.8810.90497.04190.344
1.845-1.8980.372560.31711400.3212110.8960.91598.76140.317
1.898-1.9560.391590.33511040.33811850.8640.90798.14350.331
1.956-2.020.254530.28710790.28511340.9540.93899.82360.273
2.02-2.0910.331620.2710520.27411210.910.94899.37560.256
2.091-2.1690.258400.22910260.2310670.9610.96699.90630.205
2.169-2.2570.282530.2469740.24810320.9510.95999.51550.226
2.257-2.3570.281580.2219550.22410160.950.97199.70470.2
2.357-2.4710.277510.2138940.2179480.9560.97499.68350.192
2.471-2.6040.226420.2118610.2129070.9720.9799.5590.191
2.604-2.7610.265310.218330.2128640.9460.9721000.189
2.761-2.950.313400.2157700.2198100.9470.9691000.198
2.95-3.1830.268450.2187170.2217620.9550.971000.204
3.183-3.4830.27330.2286770.237120.9650.96899.71910.217
3.483-3.8880.297390.2136160.2186550.9490.971000.205
3.888-4.4760.207280.1795460.1815740.9710.9791000.183
4.476-5.4520.381200.1834790.1895000.9290.9899.80.193
5.452-7.5850.187150.2293880.2274060.9750.96999.26110.227
7.585-29.850.192130.2172420.2162550.9580.9681000.244
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)
10.18980.0563-0.63294.5365-1.02762.3078-0.0322-0.04340.0479-0.6390.19540.01930.32450.0868-0.16310.268-0.0596-0.03140.029-0.00780.0201-10.3117-3.7673-5.4841
20.54940.04170.3931.4887-0.24720.7662-0.02580.05810.109-0.1971-0.0655-0.15670.0432-0.01380.09130.17620.01120.03590.02710.02830.0592-11.52716.0583-15.4487
Refinement TLS groupSelection: ALL

+
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