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- PDB-6co1: Structure of human TIRR in complex with 53BP1 Tudor domains -

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Basic information

Entry
Database: PDB / ID: 6co1
TitleStructure of human TIRR in complex with 53BP1 Tudor domains
Components
  • TP53-binding protein 1
  • Tudor-interacting repair regulator protein
KeywordsPROTEIN BINDING / DNA damage response / DNA repair / DNA damage signaling / 53BP1 / TIRR / NUDT16L1
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / snoRNA binding / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination ...negative regulation of double-strand break repair via nonhomologous end joining / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / snoRNA binding / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / protein homooligomerization / G2/M DNA damage checkpoint / 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 / histone binding / Processing of DNA double-strand break ends / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase ...: / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / breast cancer carboxy-terminal domain / NUDIX hydrolase-like domain superfamily / BRCT domain profile. / 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 / Tudor-interacting repair regulator protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.179 Å
AuthorsCui, G. / Botuyan, M.V. / 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 ResearchW81XWH-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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Tudor-interacting repair regulator protein
B: Tudor-interacting repair regulator protein
C: Tudor-interacting repair regulator protein
D: Tudor-interacting repair regulator protein
E: TP53-binding protein 1
F: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)120,0456
Polymers120,0456
Non-polymers00
Water18,3751020
1
A: Tudor-interacting repair regulator protein
B: Tudor-interacting repair regulator protein
E: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)60,0233
Polymers60,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tudor-interacting repair regulator protein
D: Tudor-interacting repair regulator protein
F: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)60,0233
Polymers60,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.840, 77.030, 77.240
Angle α, β, γ (deg.)85.24, 86.07, 86.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tudor-interacting repair regulator protein / NUDT16-like protein 1 / Protein syndesmos


Mass: 23038.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16L1, SDOS, TIRR / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRJ7
#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 / Water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol

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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: 2.179→46.627 Å / Num. obs: 73587 / % possible obs: 99.56 % / Redundancy: 14.4 % / Biso Wilson estimate: 23.29 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 17.9
Reflection shellResolution: 2.179→2.257 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 7203 / % possible all: 97.72

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3R, 3KVH

2g3r

3kvh


Resolution: 2.179→38.31 Å / Cross valid method: FREE R-VALUE / σ(F): 2.17 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2033 1996 2.73 %
Rwork0.1636 --
obs0.1669 73587 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.179→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 0 1020 9236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028667
X-RAY DIFFRACTIONf_angle_d0.4611721
X-RAY DIFFRACTIONf_dihedral_angle_d12.0783267
X-RAY DIFFRACTIONf_chiral_restr0.0381268
X-RAY DIFFRACTIONf_plane_restr0.0031525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1809-2.23540.33331400.23855069X-RAY DIFFRACTION96
2.2354-2.29580.27311430.19825127X-RAY DIFFRACTION97
2.2958-2.36340.24491440.18635113X-RAY DIFFRACTION97
2.3634-2.43960.22341420.18045094X-RAY DIFFRACTION97
2.4396-2.52680.23951400.17425128X-RAY DIFFRACTION97
2.5268-2.6280.21061390.16975111X-RAY DIFFRACTION97
2.628-2.74760.22951460.16485131X-RAY DIFFRACTION97
2.7476-2.89240.22151440.15775142X-RAY DIFFRACTION97
2.8924-3.07350.2131440.15845110X-RAY DIFFRACTION97
3.0735-3.31070.23391420.15955065X-RAY DIFFRACTION97
3.3107-3.64370.19111430.14985154X-RAY DIFFRACTION97
3.6437-4.17050.15971410.13585113X-RAY DIFFRACTION97
4.1705-5.25240.12181440.13155079X-RAY DIFFRACTION97
5.2524-39.83940.23361450.22415119X-RAY DIFFRACTION97
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)
11.19860.8011.47083.0397-0.49653.6035-0.05570.1087-0.1103-0.07480.2955-0.10840.1326-0.0205-0.15140.0932-0.0054-0.05580.1717-0.03260.1188-28.7539-35.605724.6377
21.28520.0755-0.3970.3974-0.09680.85220.00060.07710.1704-0.07090.00630.0335-0.03890.0624-0.00560.110.0042-0.0240.09790.00750.0729-13.9653-28.025414.7071
33.0561-1.24630.81832.23560.77824.1129-0.0120.22960.4473-0.2983-0.0108-0.0033-0.27180.16170.02930.0677-0.01040.02710.17210.00150.1545-24.2697-25.957714.8291
41.83180.5599-0.83910.4180.23251.7682-0.10640.12370.0941-0.14860.0273-0.05660.0224-0.04190.06460.07790.0154-0.02990.05720.01530.1038-15.1061-27.106815.2413
52.90890.691.7342.34520.63255.4165-0.0949-0.15750.25080.04060.135-0.1691-0.5646-0.11020.03050.11280.0182-0.03420.110.02280.1144-5.302-24.468518.0267
60.5566-0.501-0.44061.9161-0.38990.8735-0.00240.1633-0.1277-0.40970.0844-0.08890.04720.1213-0.30830.18490.0168-0.0390.2318-0.12130.0924-2.9068-45.01472.9202
73.334-0.6806-0.26762.60570.61361.817-0.00620.0373-0.0395-0.03930.07080.167-0.0007-0.0777-0.0480.0633-0.0144-0.00940.07440.00040.0483-13.6556-39.951812.6435
81.42790.6143-0.42474.9955-0.09443.53280.1259-0.071-0.24420.3036-0.3642-0.41020.45780.2059-0.08350.3031-0.0017-0.03150.0806-0.00590.3592-5.7693-50.729713.6317
91.8638-0.25490.59340.3649-0.15660.2062-0.00610.2498-0.07720.010.0929-0.10770.06790.17080.10440.19320.1242-0.1140.4975-0.16520.426725.0597-42.905412.4069
100.90650.19220.71261.43770.15790.7674-0.04290.20850.1733-0.02470.0310.0090.1780.01950.02080.0640.0132-0.01890.1863-0.01460.086110.7387-29.54913.2156
111.17930.15570.65632.03610.50351.69690.03340.3249-0.1083-0.25520.02690.06750.08490.1934-0.00930.09210.0276-0.05680.3689-0.06740.088518.7971-32.338511.7124
121.35210.19430.61281.5218-0.35390.8975-0.01010.00770.128-0.02230.0692-0.06210.00550.134-0.01240.07230.0144-0.00920.1661-0.0260.05485.6947-30.181119.293
133.58051.90790.30766.8212-0.35174.50770.3433-0.3572-0.6355-0.00130.12020.34580.6733-0.2541-0.29820.30040.0174-0.14160.19980.07790.28372.1613-44.018829.9092
142.17681.1054-0.65610.6-0.52651.1582-0.1103-0.1245-0.2295-0.0389-0.1787-0.12420.2091-0.0887-0.62520.2412-0.14010.16710.3391-0.22230.5554-38.71562.88254.4469
151.02960.09920.24781.57070.39540.861-0.03790.07530.0679-0.09410.01920.2298-0.0675-0.05620.05440.0819-0.01750.01770.0602-0.01830.1903-25.00611.888940.6169
162.4956-1.1535-3.67212.99130.81555.7185-0.0325-0.47280.3880.35520.2013-0.22240.06460.6579-0.56310.1035-0.01430.07850.2-0.10440.3556-34.00722.952251.3357
171.75050.3156-0.16121.2946-0.19440.83720.0433-0.1615-0.09450.0884-0.13190.07930.08790.08620.06720.088-0.03230.01780.0745-0.0220.1451-19.6816-6.652745.8231
185.82220.1828-1.46662.6771-0.10934.15680.1886-0.19140.21250.2149-0.3091-0.1463-0.2882-0.06780.02770.1404-0.06240.00020.15950.02670.150314.9453-10.437548.6852
190.5005-0.15990.01621.25050.20450.2884-0.02480.06260.06130.1045-0.00590.0448-0.01230.02320.0140.0981-0.03580.00760.0630.00960.1152-0.76780.515442.1705
205.19422.8044-1.53614.77441.4193.5957-0.12370.58040.3331-0.33660.21210.1698-0.4215-0.3033-0.0420.2048-0.011-0.00180.1320.02120.0955.4704-4.731.719
210.5883-1.28190.44345.5194-2.04231.2218-0.02280.05610.1364-0.09820.0797-0.19690.03190.0453-0.01060.0938-0.0458-0.00560.0871-0.02890.1339.2999-4.598443.9432
222.06740.7026-0.83661.6285-0.23962.8683-0.12560.22540.0472-0.13850.0334-0.2373-0.0955-0.08290.03520.0821-0.02180.00740.07180.01620.1308-6.80880.927833.9443
232.9841-0.48-0.61874.2902-0.33243.61750.1628-0.0790.75920.1254-0.33110.109-0.7699-0.06890.01610.1871-0.005-0.01930.1296-0.01850.3342-10.627512.135256.1228
241.45180.164-0.56480.7256-0.25360.32290.0349-0.07230.08920.0496-0.0021-0.04940.05930.0108-0.00180.1364-0.03710.00880.04390.00220.1672-0.01822.30451.9495
254.73142.5821-0.74545.9721-0.11023.66910.5088-0.9461-0.07430.8501-0.37230.59270.2377-0.3536-0.12220.3086-0.1105-0.01590.39190.03290.2648-8.60911.172462.8038
262.8385-0.5499-1.16954.10630.14116.3937-0.1939-0.0701-0.27860.13140.26650.81960.7381-0.6495-0.41750.2254-0.00320.07760.18530.1680.319-38.4955-48.184241.3607
271.8926-1.04860.84552.7212-1.20491.63890.07950.1122-0.0334-0.16450.11340.34760.1148-0.1352-0.10460.11730.0143-0.0020.08130.0720.1378-32.7587-45.060333.4764
282.32260.28881.43572.1136-0.67894.21460.01640.0757-0.00710.17870.20790.2131-0.0307-0.2913-0.18770.09-0.01980.02550.05770.03560.1923-30.0838-48.957440.3313
295.9786-0.5634-2.84671.14672.32465.22210.02160.20221.4949-0.1771-0.1295-0.4288-1.32120.6268-0.25060.3985-0.0897-0.13040.25850.03330.4817-15.7675-36.712142.8672
305.92571.058-2.29952.19460.6546.2980.1824-0.16380.70330.24420.0192-0.1143-0.6176-0.1637-0.21640.28670.0392-0.08710.06670.00570.2515-20.313-40.335149.9588
317.27090.539-3.02916.69964.28256.2640.26380.19540.3649-0.0046-0.28510.1897-0.5184-0.48780.04610.44810.0663-0.04440.1086-0.01730.1245-23.1948-38.2551.1669
320.01640.05450.0740.19370.20630.6747-0.0772-0.23020.21670.27190.0891-0.2358-0.2694-0.03520.06270.28590.0613-0.07150.1539-0.09880.2019-19.0447-39.32548.0005
330.9735-0.08560.34721.28630.8022.08060.1228-0.1025-0.28410.23160.15460.12590.377-0.0126-0.04150.13970.0317-0.00570.07730.04640.2315-25.1371-55.529540.4998
345.21340.23020.16533.34690.75572.0099-0.0793-0.2553-0.08910.1470.0249-0.4256-0.03090.4536-0.00310.102-0.02830.02860.18230.04690.126317.9354-21.516759.8886
351.589-0.95981.13691.5838-0.26470.99180.0997-0.40770.15480.1933-0.0892-0.4558-0.21170.46160.04050.1266-0.0755-0.00390.37430.02310.207522.772-18.482958.535
361.49670.4438-0.85871.0174-0.81491.2847-0.1447-0.0274-0.1133-0.0854-0.1115-0.2280.15570.28960.12520.1537-0.01390.05130.25130.05780.083215.9379-25.161663.1118
372.9727-0.669-0.38172.9112-0.41024.4124-0.01630.5512-0.3564-0.3723-0.08610.31360.2613-0.18890.32160.3221-0.0337-0.00420.1666-0.08280.12551.7359-28.479651.1484
380.72360.41490.43830.91140.21780.82050.00950.07-0.076-0.1757-0.04670.04480.20460.04320.03710.3212-0.04990.0240.1249-0.10220.12425.8673-35.426455.1315
392.83630.45830.65021.99230.83052.0589-0.0476-0.0542-0.255-0.1422-0.1144-0.04890.4130.0014-0.07640.2013-0.01820.04940.1036-0.01830.09147.8693-30.726759.4629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 146 )
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 184 )
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 206 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 24 )
10X-RAY DIFFRACTION10chain 'B' and (resid 25 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 118 )
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 184 )
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 205 )
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 24 )
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 92 )
16X-RAY DIFFRACTION16chain 'C' and (resid 93 through 107 )
17X-RAY DIFFRACTION17chain 'C' and (resid 108 through 207 )
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 24 )
19X-RAY DIFFRACTION19chain 'D' and (resid 25 through 73 )
20X-RAY DIFFRACTION20chain 'D' and (resid 74 through 92 )
21X-RAY DIFFRACTION21chain 'D' and (resid 93 through 118 )
22X-RAY DIFFRACTION22chain 'D' and (resid 119 through 146 )
23X-RAY DIFFRACTION23chain 'D' and (resid 147 through 156 )
24X-RAY DIFFRACTION24chain 'D' and (resid 157 through 184 )
25X-RAY DIFFRACTION25chain 'D' and (resid 185 through 206 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1484 through 1493 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1494 through 1523 )
28X-RAY DIFFRACTION28chain 'E' and (resid 1524 through 1542 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1543 through 1551 )
30X-RAY DIFFRACTION30chain 'E' and (resid 1552 through 1564 )
31X-RAY DIFFRACTION31chain 'E' and (resid 1565 through 1574 )
32X-RAY DIFFRACTION32chain 'E' and (resid 1575 through 1589 )
33X-RAY DIFFRACTION33chain 'E' and (resid 1590 through 1603 )
34X-RAY DIFFRACTION34chain 'F' and (resid 1485 through 1508 )
35X-RAY DIFFRACTION35chain 'F' and (resid 1509 through 1523 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1524 through 1542 )
37X-RAY DIFFRACTION37chain 'F' and (resid 1543 through 1551 )
38X-RAY DIFFRACTION38chain 'F' and (resid 1552 through 1564 )
39X-RAY DIFFRACTION39chain 'F' and (resid 1565 through 1603 )

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