[English] 日本語
Yorodumi
- PDB-6co2: Structure of an engineered protein (NUDT16TI) in complex with 53B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6co2
TitleStructure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains
Components
  • NUDT16-Tudor-interacting (NUDT16TI)
  • TP53-binding protein 1
KeywordsPROTEIN BINDING / Designer protein / Engineered protein / NUDT16TI / NUDT16 / 53BP1 / TIRR / Tudor domain / RNA binding / RNA nucleotide diphosphatase
Function / homology
Function and homology information


inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / dITP diphosphatase activity / negative regulation of rRNA processing / phosphodiesterase decapping endonuclease activity ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / dITP diphosphatase activity / negative regulation of rRNA processing / phosphodiesterase decapping endonuclease activity / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / NAD-cap decapping / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / histone H4K20me2 reader activity / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / chloride ion binding / cobalt ion binding / snoRNA binding / telomeric DNA binding / mRNA catabolic process / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / : / positive regulation of DNA-binding transcription factor activity / DNA damage checkpoint signaling / replication fork / histone reader activity / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / 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 / manganese ion binding / site of double-strand break / Processing of DNA double-strand break ends / RNA polymerase II-specific DNA-binding transcription factor binding / histone binding / damaged DNA binding / chromosome, telomeric region / nuclear body / nucleotide binding / mRNA binding / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / U8 snoRNA-decapping enzyme-like / Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 ...: / U8 snoRNA-decapping enzyme-like / Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / breast cancer carboxy-terminal domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / BRCT domain profile. / NUDIX hydrolase-like domain superfamily / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TP53-binding protein 1 / U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsBotuyan, M.V. / Thompson, J.R. / Cui, G. / Mer, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116829 United States
Department of Defense Ovarian Cancer Research ProgramW81XWH-16-1-0391 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein.
Authors: Botuyan, M.V. / Cui, G. / Drane, P. / Oliveira, C. / Detappe, A. / Brault, M.E. / Parnandi, N. / Chaubey, S. / Thompson, J.R. / Bragantini, B. / Zhao, D. / Chapman, J.R. / Chowdhury, D. / Mer, G.
History
DepositionMar 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUDT16-Tudor-interacting (NUDT16TI)
B: NUDT16-Tudor-interacting (NUDT16TI)
C: TP53-binding protein 1
D: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)70,9714
Polymers70,9714
Non-polymers00
Water5,639313
1
A: NUDT16-Tudor-interacting (NUDT16TI)
B: NUDT16-Tudor-interacting (NUDT16TI)
C: TP53-binding protein 1

D: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)70,9714
Polymers70,9714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z+1/41
Unit cell
Length a, b, c (Å)73.689, 73.689, 276.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein NUDT16-Tudor-interacting (NUDT16TI)


Mass: 21540.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Engineered protein / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pBB75 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase
#2: Protein TP53-binding protein 1 / p53BP1


Mass: 13944.780 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dehydrate, pH 5.6, 0.2 M ammonium acetate, 10% PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.49→44.225 Å / Num. obs: 27761 / % possible obs: 99.88 % / Redundancy: 42.9 % / Biso Wilson estimate: 29.14 Å2 / Rmerge(I) obs: 0.1274 / Net I/σ(I): 20.47
Reflection shellResolution: 2.49→2.579 Å / Redundancy: 30.4 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 2689 / % possible all: 99.63

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3R, 2XSQ

2g3r

2xsq


Resolution: 2.49→44.225 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1742 6.28 %
Rwork0.2195 --
obs0.2227 27750 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→44.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 0 313 4900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024741
X-RAY DIFFRACTIONf_angle_d0.436398
X-RAY DIFFRACTIONf_dihedral_angle_d11.0582797
X-RAY DIFFRACTIONf_chiral_restr0.04681
X-RAY DIFFRACTIONf_plane_restr0.002840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.56330.31821400.29982092X-RAY DIFFRACTION100
2.5633-2.6460.35031420.28392127X-RAY DIFFRACTION100
2.646-2.74060.30371430.28522133X-RAY DIFFRACTION100
2.7406-2.85030.30311420.25782108X-RAY DIFFRACTION100
2.8503-2.980.29341420.25062138X-RAY DIFFRACTION100
2.98-3.1370.28271430.23772124X-RAY DIFFRACTION100
3.137-3.33350.2931450.21252159X-RAY DIFFRACTION100
3.3335-3.59080.27321440.20942143X-RAY DIFFRACTION100
3.5908-3.95190.23831450.19622169X-RAY DIFFRACTION100
3.9519-4.52330.22331470.1632197X-RAY DIFFRACTION100
4.5233-5.6970.2231510.17992240X-RAY DIFFRACTION100
5.697-44.23210.28811580.23482378X-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)
11.741-0.66070.69294.15272.72595.01160.0081-0.16370.09420.1931-0.0797-0.05880.08430.1081-0.00360.5037-0.03980.07320.16150.02470.1785-29.23084.195922.2588
20.0150.07520.0210.41440.11840.03490.10430.3189-0.4397-0.1498-0.0274-0.22190.83710.37210.00670.92370.17510.0940.3925-0.22820.229-27.4318-10.3121-2.9579
31.6936-0.18010.02732.2614-1.72794.98060.1067-0.1438-0.18980.3894-0.2390.6751-0.2805-0.8123-0.00070.4988-0.13440.10440.3022-0.06390.3072-39.74912.616915.8625
41.63141.24590.63984.76182.13772.8298-0.20830.1794-0.01430.01620.30260.29720.4378-0.27140.06030.5168-0.17090.07410.2591-0.03880.2047-32.93970.871518.9841
53.2645-1.21370.12750.4516-0.02141.23650.08980.3591-0.2615-0.264-0.1593-0.0740.4563-0.0768-0.05170.6072-0.12880.05680.1601-0.00930.1657-30.8601-2.573817.1106
61.4540.2450.7261.8345-0.23382.59340.16220.1274-0.12850.2473-0.2205-0.06060.7841-0.21390.0790.4303-0.09530.03930.4512-0.07570.1062-33.9408-1.47791.5026
74.3699-1.56191.2434.6698-1.6875.05160.30570.39070.07850.4869-0.2523-0.16210.25030.69080.05850.45310.1254-0.10380.4747-0.05520.2614-21.9414-1.2479.1581
81.10050.0167-0.63060.7696-0.1461.1702-0.1039-0.28940.3060.2598-0.09950.1115-0.3913-0.6198-0.54510.11560.24660.2590.7574-0.2218-0.0024-40.9219.4848-17.0009
92.83460.2403-0.27930.7741-1.31032.4747-0.1264-0.0272-0.0783-0.02960.01890.17340.1312-0.28540.14120.2425-0.0410.08430.5067-0.09350.1848-37.76192.306-13.3189
101.76410.0045-0.5621.1385-0.42160.6267-0.10540.2541-0.16620.0739-0.02470.28310.1624-0.9939-0.0044-0.0261-0.11080.10.8266-0.20530.2514-42.30372.6837-20.2438
111.9604-0.54840.36981.54950.49263.1624-0.11050.25390.15040.29620.04250.1039-0.2842-0.7410.12260.4069-0.00640.03580.4078-0.03110.1388-40.36547.9396-5.8874
122.9182-0.37190.53234.4641-1.66522.46680.01440.02470.5237-0.13190.0067-0.158-0.7324-0.3621-0.02730.2870.05580.04110.1709-0.00780.2547-20.530117.2242-34.5199
135.5182-0.2493-1.86190.91630.12283.0764-0.0726-0.3643-0.19440.06110.1146-0.06680.06670.14570.00290.1351-0.0620.00450.21420.01260.2482-10.15384.6449-28.5182
144.23440.6756-0.91893.392-0.17552.49770.0139-0.48390.05780.29330.13080.1543-0.21840.39140.04210.1287-0.05610.00430.2110.02450.2628-9.63066.8851-28.2847
156.08982.23092.31635.4682.1021.22290.10490.13620.4513-0.44010.32120.0542-0.52560.4799-0.53950.160.04540.05580.3997-0.01560.302413.218115.0274-43.2779
166.7170.6981-0.11891.8834-1.37953.448-0.03290.07060.37420.0787-0.0602-0.0536-0.37080.16430.12010.14740.02070.02040.3397-0.04860.226312.648913.3017-41.4816
176.4961.182-1.92844.27340.33742.9344-0.14830.363-0.3753-0.2811-0.01790.12090.0572-0.16970.15730.13250.01210.01890.4005-0.03180.23164.94534.0382-43.7227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 167 )
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 182 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 117 )
11X-RAY DIFFRACTION11chain 'B' and (resid 118 through 182 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1485 through 1531 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1532 through 1564 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1565 through 1602 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1486 through 1501 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1502 through 1552 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1553 through 1603 )

+
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