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- PDB-6wlg: Ints3 C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 6wlg
TitleInts3 C-terminal Domain
ComponentsIntegrator complex subunit 3
KeywordsPROTEIN BINDING / DNA damage repair / snRNA processing / HEAT repeat
Function / homology
Function and homology information


SOSS complex / 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 / site of double-strand break / DNA repair ...SOSS complex / 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 / 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
Similarity search - Domain/homology
Integrator complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.111 Å
AuthorsLi, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for multifunctional roles of human Ints3 C-terminal domain.
Authors: Li, J. / Ma, X. / Banerjee, S. / Baruah, S. / Schnicker, N.J. / Roh, E. / Ma, W. / Liu, K. / Bode, A.M. / Dong, Z.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,9322
Polymers97,9322
Non-polymers00
Water00
1
A: Integrator complex subunit 3

B: Integrator complex subunit 3


Theoretical massNumber of molelcules
Total (without water)97,9322
Polymers97,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3550 Å2
ΔGint-17 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.854, 234.854, 47.567
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU(chain 'A' and (resid 576 through 607 or resid 612...AA576 - 58523 - 32
12ALAALALEULEU(chain 'A' and (resid 576 through 607 or resid 612...AA593 - 60640 - 53
13SERSERGLNGLN(chain 'A' and (resid 576 through 607 or resid 612...AA612 - 62359 - 70
14VALVALCYSCYS(chain 'A' and (resid 576 through 607 or resid 612...AA634 - 66081 - 107
15SERSERARGARG(chain 'A' and (resid 576 through 607 or resid 612...AA667 - 695114 - 142
16ALAALAALAALA(chain 'A' and (resid 576 through 607 or resid 612...AA700 - 713147 - 160
17LEULEULYSLYS(chain 'A' and (resid 576 through 607 or resid 612...AA719 - 897166 - 344
18GLNGLNGLNGLN(chain 'A' and (resid 576 through 607 or resid 612...AA917 - 955364 - 402
19ALAALAGLUGLU(chain 'A' and (resid 576 through 607 or resid 612...AA961 - 974408 - 421
21GLUGLULEULEUchain 'B'BB576 - 58523 - 32
22ALAALALEULEUchain 'B'BB593 - 60640 - 53
23SERSERGLNGLNchain 'B'BB612 - 62359 - 70
24VALVALCYSCYSchain 'B'BB634 - 66081 - 107
25SERSERARGARGchain 'B'BB667 - 695114 - 142
26ALAALAALAALAchain 'B'BB700 - 713147 - 160
27LEULEULYSLYSchain 'B'BB719 - 897166 - 344
28GLNGLNGLNGLNchain 'B'BB917 - 955364 - 402
29ALAALAGLUGLUchain 'B'BB961 - 974408 - 421

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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: 48966.109 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

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Acetate, 13% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.11→46.32 Å / Num. obs: 17495 / % possible obs: 99.5 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 3.11→3.33 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3181 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.111→46.317 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2633 825 4.72 %
Rwork0.2037 --
obs0.2065 17485 99.45 %
Refinement stepCycle: LAST / Resolution: 3.111→46.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 0 0 5750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335842
X-RAY DIFFRACTIONf_angle_d0.77667883
X-RAY DIFFRACTIONf_chiral_restr0.0416923
X-RAY DIFFRACTIONf_plane_restr0.0041995
X-RAY DIFFRACTIONf_dihedral_angle_d2.68533604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.310.35571460.27092759X-RAY DIFFRACTION99.11
3.31-3.560.26981510.21482787X-RAY DIFFRACTION99.93
3.56-3.920.27551290.20662800X-RAY DIFFRACTION99.93
3.92-4.490.24161290.17532765X-RAY DIFFRACTION99.08
4.49-5.650.23351450.2052782X-RAY DIFFRACTION100
5.65-46.320.27641250.20512767X-RAY DIFFRACTION98.67
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)
18.85723736291-3.763935856421.409501124733.79242561294-0.3453576142192.21642873694-0.624780964106-0.5205273203420.4744315587060.5291804036250.625929514353-0.8469248618810.2656910008850.7692123951080.1022030459210.7019138361710.154331862019-0.1102674488240.934803713961-0.1441999255420.7001106298640.7359293532-3.7523340767912.552770823
23.12630660963-1.4306075457-0.2555293121469.19614157031-0.4073279246662.625490291510.3672642283250.467118622770.594823801741-0.835710574103-0.466281447501-0.890603226187-0.3794861259460.1329895903310.1076802792380.652651894006-0.01206298561750.1875855261550.9830864339720.16578182590.80339811702235.02695098899.4307918410434.6614056085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 571:976)
2X-RAY DIFFRACTION2(chain B and resseq 576:975)

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