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- PDB-5jjx: Crystal structure of the HAT domain of sart3 -

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Basic information

Entry
Database: PDB / ID: 5jjx
TitleCrystal structure of the HAT domain of sart3
ComponentsSquamous cell carcinoma antigen recognized by T-cells 3
KeywordsIMMUNE SYSTEM / SART3 / HAT / Structural Genomics / Structural Genomics Consortium / SGC
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 / U6 snRNA binding / spliceosomal snRNP assembly ...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 / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / 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 / Resolution: 2 Å
AuthorsDONG, A. / ZHANG, Q. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the HAT domain of sart3
Authors: ZHANG, Q. / DONG, A. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _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

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Assembly

Deposited unit
A: Squamous cell carcinoma antigen recognized by T-cells 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,24814
Polymers37,2121
Non-polymers3513
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area15400 Å2
2
A: Squamous cell carcinoma antigen recognized by T-cells 3
hetero molecules

A: Squamous cell carcinoma antigen recognized by T-cells 3
hetero molecules

A: Squamous cell carcinoma antigen recognized by T-cells 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,74342
Polymers111,6373
Non-polymers10639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4260 Å2
ΔGint-57 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.113, 135.113, 43.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-408-

UNX

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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: 37212.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q15020
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 3350, 0.2 M NaCl, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30852 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.025 / Rrim(I) all: 0.069 / Χ2: 1.636 / Net I/av σ(I): 43.543 / Net I/σ(I): 12.6 / Num. measured all: 256972
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.037.80.9681100
2.03-2.078.10.8961100
2.07-2.1180.6821100
2.11-2.158.20.5151100
2.15-2.28.10.4491100
2.2-2.258.20.3421100
2.25-2.318.20.291100
2.31-2.378.20.2471100
2.37-2.448.30.1941100
2.44-2.528.40.1721100
2.52-2.618.30.1521100
2.61-2.718.50.1421100
2.71-2.848.50.1181100
2.84-2.998.60.0931100
2.99-3.178.70.0691100
3.17-3.428.70.0531100
3.42-3.768.50.0571100
3.76-4.318.30.051100
4.31-5.438.50.0411100
5.43-508.20.032199.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
SOLVEphasing
RefinementResolution: 2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.016 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.141
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1004 3.3 %RANDOM
Rwork0.2067 ---
obs0.2077 29831 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.04 Å2 / Biso mean: 45.951 Å2 / Biso min: 26.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 13 121 2526
Biso mean--31.72 45.26 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192473
X-RAY DIFFRACTIONr_bond_other_d0.0010.022297
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9533357
X-RAY DIFFRACTIONr_angle_other_deg0.93135251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33923.504117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9321519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
X-RAY DIFFRACTIONr_mcbond_it2.4054.671208
X-RAY DIFFRACTIONr_mcbond_other2.3884.6671207
X-RAY DIFFRACTIONr_mcangle_it3.4896.9811510
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 72 -
Rwork0.283 2181 -
all-2253 -
obs--99.43 %

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