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- PDB-6co2: Structure of an engineered protein (NUDT16TI) in complex with 53B... -

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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 / ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / Phosphate bond hydrolysis by NUDT proteins / cellular response to X-ray / metalloexopeptidase activity / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / cobalt ion binding / chloride ion binding / snoRNA binding / telomeric DNA binding / : / mRNA catabolic process / histone reader activity / SUMOylation of transcription factors / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of double-strand break repair via homologous recombination / DNA damage checkpoint signaling / replication fork / 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 / manganese ion 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 / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.64 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

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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

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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 )

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