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- PDB-5ctt: Crystal structure of human SART3/TIP110 NLS-mouse importin alpha ... -

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Basic information

Entry
Database: PDB / ID: 5ctt
TitleCrystal structure of human SART3/TIP110 NLS-mouse importin alpha complex
Components
  • Importin subunit alpha-1
  • Squamous cell carcinoma antigen recognized by T-cells 3
KeywordsTRANSPORT PROTEIN / IMMUNE SYSTEM / NUCLEAR PROTEIN / RNA BINDING PROTEIN / Nuclear localization signal / Complex / Protein Transporter
Function / homology
Function and homology information


U6atac snRNA binding / ASAP complex / regulation of RNA metabolic process / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / U4 snRNA binding / nuclear import signal receptor activity ...U6atac snRNA binding / ASAP complex / regulation of RNA metabolic process / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / U4 snRNA binding / nuclear import signal receptor activity / transcription elongation-coupled chromatin remodeling / hematopoietic stem cell proliferation / ubiquitin-specific protease binding / spliceosomal tri-snRNP complex assembly / homeostasis of number of cells / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / mRNA splicing, via spliceosome / cell morphogenesis / cytoplasmic stress granule / protein import into nucleus / nucleosome assembly / host cell / regulation of gene expression / protein-macromolecule adaptor activity / histone binding / DNA-binding transcription factor binding / postsynaptic density / nuclear speck / glutamatergic synapse / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / PRP39 C-terminal HAT repeat / PRP39 N-terminal HAT repeat / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / PRP39 C-terminal HAT repeat / PRP39 N-terminal HAT repeat / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Spliceosome associated factor 3, U4/U6 recycling protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPark, J.K. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2011-0021713 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3
Authors: Park, J.K. / Das, T. / Song, E.J. / Kim, E.E.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)54,9822
Polymers54,9822
Non-polymers00
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint8 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.149, 89.992, 97.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 48446.379 Da / Num. of mol.: 1 / Fragment: UNP residues 72-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein Squamous cell carcinoma antigen recognized by T-cells 3 / SART-3 / Tat-interacting protein of 110 kDa / Tip110 / p110 nuclear RNA-binding protein


Mass: 6535.394 Da / Num. of mol.: 1 / Fragment: UNP residues 601-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15020
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES, pH 6.6, 1.6M sodium citrate, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 77648 / % possible obs: 99 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.96 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAL

1ial


Resolution: 1.7→37.765 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1993 2.6 %
Rwork0.191 --
obs0.1918 76791 98.93 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.684 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0058 Å2-0 Å20 Å2
2---2.9274 Å2-0 Å2
3---3.9332 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 472 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073454
X-RAY DIFFRACTIONf_angle_d1.0944699
X-RAY DIFFRACTIONf_dihedral_angle_d13.2081281
X-RAY DIFFRACTIONf_chiral_restr0.074562
X-RAY DIFFRACTIONf_plane_restr0.005604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6984-1.74090.35981270.34915117X-RAY DIFFRACTION96
1.7409-1.7880.36351410.32985199X-RAY DIFFRACTION98
1.788-1.84060.31011410.29745274X-RAY DIFFRACTION98
1.8406-1.90.25891410.25545242X-RAY DIFFRACTION99
1.9-1.96790.27061420.23525301X-RAY DIFFRACTION99
1.9679-2.04670.25411460.20775319X-RAY DIFFRACTION99
2.0467-2.13980.21111330.18195353X-RAY DIFFRACTION99
2.1398-2.25260.20151450.17145317X-RAY DIFFRACTION99
2.2526-2.39380.18931430.1675348X-RAY DIFFRACTION100
2.3938-2.57850.21071430.17675375X-RAY DIFFRACTION100
2.5785-2.8380.23361500.18555386X-RAY DIFFRACTION100
2.838-3.24840.25331420.1815435X-RAY DIFFRACTION100
3.2484-4.09190.17261480.16015495X-RAY DIFFRACTION100
4.0919-37.77470.18111510.1685637X-RAY DIFFRACTION99

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