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- PDB-6sn1: Crystal structure of the human INTS13-INTS14 complex -

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Basic information

Entry
Database: PDB / ID: 6sn1
TitleCrystal structure of the human INTS13-INTS14 complex
Components
  • Integrator complex subunit 13
  • Integrator complex subunit 14
KeywordsRNA BINDING PROTEIN / Integrator / Interlocked chains / VWA / pseudosymmetrical heterodimer
Function / homology
Function and homology information


regulation of fertilization / snRNA processing / integrator complex / snRNA 3'-end processing / flagellated sperm motility / protein localization to nuclear envelope / regulation of transcription elongation by RNA polymerase II / centrosome localization / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle ...regulation of fertilization / snRNA processing / integrator complex / snRNA 3'-end processing / flagellated sperm motility / protein localization to nuclear envelope / regulation of transcription elongation by RNA polymerase II / centrosome localization / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle / mitotic spindle organization / nuclear body / cell division / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cell cycle regulator Mat89Bb / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Cell cycle and development regulator Mat89Bb / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / von Willebrand factor type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrator complex subunit 14 / Integrator complex subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsJonas, S. / Sabath, K. / Staeubli, M.L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182880 Switzerland
CitationJournal: Nat Commun / Year: 2020
Title: INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module.
Authors: Sabath, K. / Staubli, M.L. / Marti, S. / Leitner, A. / Moes, M. / Jonas, S.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Integrator complex subunit 13
B: Integrator complex subunit 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1728
Polymers143,5962
Non-polymers5766
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-147 kcal/mol
Surface area46450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.987, 115.354, 147.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Integrator complex subunit 13 / / Cell cycle regulator Mat89Bb homolog / Germ cell tumor 1 / Protein asunder homolog / Sarcoma antigen NY-SAR-95


Mass: 86069.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVM9
#2: Protein Integrator complex subunit 14 / / von Willebrand factor A domain-containing protein 9


Mass: 57526.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS14, C15orf44, VWA9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SY0
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.67 Å3/Da / Density % sol: 78.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-Tris (pH 6.0), 0.75 M AmSO4 and 1% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→45.47 Å / Num. obs: 107306 / % possible obs: 99.49 % / Redundancy: 13.7 % / Biso Wilson estimate: 55.76 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.04 / Rrim(I) all: 0.149 / Net I/σ(I): 16.2
Reflection shellResolution: 2.54→2.63 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 10162 / CC1/2: 0.354 / Rpim(I) all: 1.012 / Rrim(I) all: 3.806 / % possible all: 95.33

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing
SHELXDphasing
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.54→45.47 Å / SU ML: 0.4516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2423
RfactorNum. reflection% reflection
Rfree0.2437 5463 5.09 %
Rwork0.2241 --
obs0.2252 107306 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81.83 Å2
Refinement stepCycle: LAST / Resolution: 2.54→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 30 90 8015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198085
X-RAY DIFFRACTIONf_angle_d0.48110989
X-RAY DIFFRACTIONf_chiral_restr0.03921268
X-RAY DIFFRACTIONf_plane_restr0.00321413
X-RAY DIFFRACTIONf_dihedral_angle_d15.84664911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.570.4681480.4712953X-RAY DIFFRACTION86.79
2.57-2.60.45581750.43683348X-RAY DIFFRACTION99.55
2.6-2.630.411740.42883364X-RAY DIFFRACTION99.72
2.63-2.670.42151700.38773368X-RAY DIFFRACTION99.8
2.67-2.70.39541940.38233366X-RAY DIFFRACTION99.97
2.7-2.740.35631790.35043370X-RAY DIFFRACTION99.75
2.74-2.780.38371620.33393393X-RAY DIFFRACTION99.94
2.78-2.820.34181750.32143395X-RAY DIFFRACTION99.89
2.82-2.860.34972110.31743314X-RAY DIFFRACTION99.83
2.86-2.910.3331890.29553400X-RAY DIFFRACTION99.86
2.91-2.960.31171720.29373382X-RAY DIFFRACTION99.97
2.96-3.010.30171690.28953410X-RAY DIFFRACTION99.94
3.01-3.070.35331830.29143359X-RAY DIFFRACTION99.97
3.07-3.130.33571730.29433410X-RAY DIFFRACTION100
3.13-3.20.30412090.27923361X-RAY DIFFRACTION99.97
3.2-3.280.26851920.26033391X-RAY DIFFRACTION100
3.28-3.360.28961780.25023404X-RAY DIFFRACTION100
3.36-3.450.27941900.2513381X-RAY DIFFRACTION99.92
3.45-3.550.25851860.24363397X-RAY DIFFRACTION100
3.55-3.670.27321920.23973411X-RAY DIFFRACTION100
3.67-3.80.23671770.22133396X-RAY DIFFRACTION99.97
3.8-3.950.24281900.21013397X-RAY DIFFRACTION99.97
3.95-4.130.20121890.18413430X-RAY DIFFRACTION100
4.13-4.350.17431650.17083447X-RAY DIFFRACTION100
4.35-4.620.20181780.16593439X-RAY DIFFRACTION100
4.62-4.970.20182020.17163412X-RAY DIFFRACTION100
4.97-5.470.1841810.18933502X-RAY DIFFRACTION100
5.47-6.260.23831750.21343456X-RAY DIFFRACTION100
6.26-7.890.21171810.20173537X-RAY DIFFRACTION100
7.89-45.470.17612040.16963650X-RAY DIFFRACTION99.66

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