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- PDB-7bv7: INTS3 complexed with INTS6 -

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Basic information

Entry
Database: PDB / ID: 7bv7
TitleINTS3 complexed with INTS6
Components
  • Integrator complex subunit 3
  • Integrator complex subunit 6
KeywordsRECOMBINATION / DNA double strand break repair INTS3 INTS6 SSB1
Function / homology
Function and homology information


SOSS complex / snRNA 3'-end processing / snRNA processing / integrator complex / regulation of transcription elongation by RNA polymerase II / mitotic G2/M transition checkpoint / response to ionizing radiation / RNA polymerase II transcribes snRNA genes / double-strand break repair via homologous recombination / transmembrane signaling receptor activity ...SOSS complex / snRNA 3'-end processing / snRNA processing / integrator complex / regulation of transcription elongation by RNA polymerase II / mitotic G2/M transition checkpoint / response to ionizing radiation / RNA polymerase II transcribes snRNA genes / double-strand break repair via homologous recombination / transmembrane signaling receptor activity / actin cytoskeleton / site of double-strand break / DNA repair / DNA damage response / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Integrator complex subunit 3, N-terminal / Integrator complex subunit 3 / Integrator complex subunit 3 N-terminal / INTS6/SAGE1/DDX26B/CT45, C-terminal / INTS6/SAGE1/DDX26B/CT45 C-terminus / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrator complex subunit 3 / Integrator complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJia, Y. / Bharath, S.R. / Song, H.
CitationJournal: Cell Discov / Year: 2021
Title: Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair.
Authors: Jia, Y. / Cheng, Z. / Bharath, S.R. / Sun, Q. / Su, N. / Huang, J. / Song, H.
History
DepositionApr 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrator complex subunit 3
B: Integrator complex subunit 3
C: Integrator complex subunit 6


Theoretical massNumber of molelcules
Total (without water)111,2443
Polymers111,2443
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.570, 126.030, 84.440
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrator complex subunit 3 / Int3 / SOSS complex subunit A / Sensor of single-strand DNA complex subunit A / Sensor of ssDNA subunit A


Mass: 50291.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS3, C1orf193, C1orf60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68E01
#2: Protein Integrator complex subunit 6 / Int6 / DBI-1 / Protein DDX26 / Protein deleted in cancer 1 / DICE1


Mass: 10660.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS6, DBI1, DDX26, DDX26A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UL03
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 1.7 M Ammonium citrate pH 7.0 4% pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.45 Å / Num. obs: 43480 / % possible obs: 90 % / Redundancy: 2.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 4704 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.95 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.2492 2124 4.89 %
Rwork0.2048 --
obs0.2069 43428 89.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.09 Å2 / Biso mean: 53.5158 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 2.4→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 0 181 6182
Biso mean---48.15 -
Num. residues----758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.30541340.25162850298493
2.46-2.520.28491670.24352782294992
2.52-2.590.29361220.24022841296392
2.59-2.660.27641540.23432819297392
2.66-2.750.31811490.23352779292891
2.75-2.850.25091340.21832809294392
2.85-2.960.26741280.20622781290991
2.96-3.090.28071550.20522795295091
3.09-3.260.23251400.20232747288790
3.26-3.460.22661490.1912720286989
3.46-3.730.23691450.18172709285488
3.73-4.10.23721530.17392676282988
4.1-4.70.20891340.17272640277485
4.7-5.910.2271380.20872664280287
5.92-43.950.26971220.23212692281485
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)
13.03380.5796-0.09521.97360.24062.0619-0.0487-0.060.62150.003-0.16350.8037-0.2712-0.48620.04870.22140.0601-0.04970.2789-0.09790.5463-24.262164.922222.5114
22.32280.4019-0.54524.29550.86531.0255-0.2515-0.0724-0.81890.6384-0.0719-0.10070.5696-0.06870.18440.74310.01330.16860.2709-0.02920.5444-2.222825.318117.099
30.5145-0.3877-0.55991.49570.18411.03710.26261.22380.0994-0.7716-0.5406-0.20190.25510.3820.20920.8180.30350.13681.50830.05130.553628.359149.9807-10.7069
43.0015-0.8887-1.06821.0055-0.77822.5750.16490.47840.0583-0.0817-0.2513-0.29620.12790.87730.02810.25320.04450.0050.6129-0.02320.257619.962450.91047.4283
51.5708-0.576-0.92772.01491.44553.8709-0.2941-0.3502-0.07330.68910.160.23770.40490.09520.11010.39220.0650.00290.2756-0.00030.2397-1.429657.660540.4465
62.6579-0.70510.32984.6553-1.40853.9508-0.00830.38420.2735-0.274-0.04670.27120.3141-0.2494-0.0070.3753-0.0454-0.03260.32940.07660.3575-7.700166.77495.4462
71.7672-0.2194-0.20932.4799-0.77984.09320.29760.37490.3529-0.1436-0.05480.5162-0.2502-0.7203-0.23410.3646-0.0023-0.04640.30820.10540.365-6.325774.99925.0367
82.3339-1.98731.19635.679-6.12137.58380.15880.46770.56590.4154-0.8063-1.6328-1.25250.80220.61160.5712-0.01760.02070.40840.10050.59011.579782.0644.4386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 595 through 850 )A595 - 850
2X-RAY DIFFRACTION2chain 'A' and (resid 851 through 972 )A851 - 972
3X-RAY DIFFRACTION3chain 'B' and (resid 583 through 667 )B583 - 667
4X-RAY DIFFRACTION4chain 'B' and (resid 668 through 781 )B668 - 781
5X-RAY DIFFRACTION5chain 'B' and (resid 782 through 972 )B782 - 972
6X-RAY DIFFRACTION6chain 'C' and (resid 808 through 827 )C808 - 827
7X-RAY DIFFRACTION7chain 'C' and (resid 828 through 860 )C828 - 860
8X-RAY DIFFRACTION8chain 'C' and (resid 861 through 881 )C861 - 881

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