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- PDB-5ctq: Crystal structure of human SART3/TIP110 half-a TPR (HAT) domain -

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Basic information

Entry
Database: PDB / ID: 5ctq
TitleCrystal structure of human SART3/TIP110 half-a TPR (HAT) domain
ComponentsSquamous cell carcinoma antigen recognized by T-cells 3
KeywordsIMMUNE SYSTEM / NUCLEAR PROTEIN / RNA BINDING PROTEIN / half a tetratricopeptide repeat (HAT) domain / Protein transporter
Function / homology
Function and homology information


U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / Cajal body / U6 snRNA binding ...U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / cell morphogenesis / mRNA splicing, via spliceosome / nucleosome assembly / histone binding / regulation of gene expression / nuclear speck / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Squamous cell carcinoma antigen recognized by T-cells 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsPark, J.K. / Kim, E.E.
Funding supportKorea, Democratic People's Republic Of, 1items
OrganizationGrant numberCountry
Global Research Laboratory program of the Ministry of Science, ICT and Future Planning20110021713Korea, Democratic People's 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 1.2Mar 20, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_audit_support / 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_audit_support.country / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Squamous cell carcinoma antigen recognized by T-cells 3
B: Squamous cell carcinoma antigen recognized by T-cells 3
C: Squamous cell carcinoma antigen recognized by T-cells 3
D: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)263,2824
Polymers263,2824
Non-polymers00
Water5,062281
1
A: Squamous cell carcinoma antigen recognized by T-cells 3
B: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)131,6412
Polymers131,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Squamous cell carcinoma antigen recognized by T-cells 3
D: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)131,6412
Polymers131,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.912, 80.529, 146.641
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 65820.547 Da / Num. of mol.: 4 / Fragment: UNP residues 94-611
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200mM sodium formate pH 7.5, 30% PEG4000

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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: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 87186 / % possible obs: 95.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.07 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→38.15 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 1988 2.42 %
Rwork0.2353 --
obs0.2364 82307 95.79 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.321 Å2 / ksol: 0.268 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3594 Å20 Å2-4.3083 Å2
2--7.7907 Å20 Å2
3----3.4312 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16635 0 0 281 16916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816977
X-RAY DIFFRACTIONf_angle_d1.45122951
X-RAY DIFFRACTIONf_dihedral_angle_d15.4656422
X-RAY DIFFRACTIONf_chiral_restr0.0742445
X-RAY DIFFRACTIONf_plane_restr0.0072977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.44521320.41555278X-RAY DIFFRACTION89
2.665-2.7370.42841320.39365390X-RAY DIFFRACTION91
2.737-2.81760.39881360.36195451X-RAY DIFFRACTION92
2.8176-2.90850.3831360.32885503X-RAY DIFFRACTION93
2.9085-3.01240.36071390.31485611X-RAY DIFFRACTION94
3.0124-3.13290.33051410.28175679X-RAY DIFFRACTION95
3.1329-3.27550.34811420.27295793X-RAY DIFFRACTION97
3.2755-3.4480.28551450.24315834X-RAY DIFFRACTION98
3.448-3.66390.26391440.21115856X-RAY DIFFRACTION98
3.6639-3.94650.22561460.18465891X-RAY DIFFRACTION99
3.9465-4.34320.25241460.18015902X-RAY DIFFRACTION98
4.3432-4.97050.24711480.19345978X-RAY DIFFRACTION99
4.9705-6.25780.2391490.21196017X-RAY DIFFRACTION99
6.2578-38.15440.22881520.19096136X-RAY DIFFRACTION99

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