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- PDB-8hpp: Crystal structure of human INTS3 with SAGE1 -

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Basic information

Entry
Database: PDB / ID: 8hpp
TitleCrystal structure of human INTS3 with SAGE1
Components
  • Integrator complex subunit 3
  • Sarcoma antigen 1
KeywordsTRANSCRIPTION / Integrator / Cancer-Testis Antigen / Tumorigenesis
Function / homology
Function and homology information


SOSS complex / snRNA processing / integrator complex / snRNA 3'-end processing / 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 ...SOSS complex / snRNA processing / integrator complex / snRNA 3'-end processing / 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 / nuclear body / 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
Similarity search - Domain/homology
Integrator complex subunit 3 / Sarcoma antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsDeng, W. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cancer-testis antigen SAGE1 is a pan-cancer master regulator of RNA polymerase II
Authors: Deng, W. / Wu, J. / Lei, M.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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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: Sarcoma antigen 1


Theoretical massNumber of molelcules
Total (without water)118,6873
Polymers118,6873
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-22 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)260.119, 46.241, 103.104
Angle α, β, γ (deg.)90.000, 113.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 53929.332 Da / Num. of mol.: 2 / Fragment: C-terminal motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS3, C1orf193, C1orf60 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q68E01
#2: Protein Sarcoma antigen 1 / Cancer/testis antigen 14 / CT14


Mass: 10827.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAGE1, SAGE / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NXZ1

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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: 2.4 Å3/Da / Density % sol: 48.74 % / Mosaicity: 0.378 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium sulfate and 25% Ethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 22718 / % possible obs: 97.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Χ2: 0.928 / Net I/σ(I): 6.2 / Num. measured all: 92299
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.113.60.51819400.794184.1
3.11-3.233.90.44921410.821192.2
3.23-3.3840.33622270.79198.2
3.38-3.564.20.24923330.848199.7
3.56-3.784.20.16523010.8711100
3.78-4.074.20.12222980.9081100
4.07-4.484.20.08323350.9551100
4.48-5.134.20.0723501.0751100
5.13-6.464.10.08223551.2291100
6.46-1003.90.03124380.914199.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3→47.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 22.214 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1101 4.9 %RANDOM
Rwork0.2152 ---
obs0.2173 21484 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 262.43 Å2 / Biso mean: 110.119 Å2 / Biso min: 34.35 Å2
Baniso -1Baniso -2Baniso -3
1--5.95 Å2-0 Å20.71 Å2
2---7.76 Å20 Å2
3---9.56 Å2
Refinement stepCycle: final / Resolution: 3→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 0 0 7102
Num. residues----875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127224
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.6259741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84824.36383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.888151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9171530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025343
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 77 -
Rwork0.291 1349 -
all-1426 -
obs--83.73 %

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