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- PDB-3tp2: Crystal Structure of the Splicing Factor Cwc2 from yeast -

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Basic information

Entry
Database: PDB / ID: 3tp2
TitleCrystal Structure of the Splicing Factor Cwc2 from yeast
ComponentsPre-mRNA-splicing factor CWC2
KeywordsSPLICING / RNA scaffold / Torus domain / CCCH zinc finger / RRM domain
Function / homology
Function and homology information


Prp19 complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / positive regulation of RNA splicing / mRNA splicing, via spliceosome ...Prp19 complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / positive regulation of RNA splicing / mRNA splicing, via spliceosome / cell cycle / metal ion binding
Similarity search - Function
Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Pre-mRNA-splicing factor Cwc2/Slt11 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Pre-mRNA-splicing factor Cwc2/Slt11 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RRM (RNA recognition motif) domain / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-splicing factor CWC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSchmitzova, J.
CitationJournal: Embo J. / Year: 2012
Title: Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein.
Authors: Schmitzova, J. / Rasche, N. / Dybkov, O. / Kramer, K. / Fabrizio, P. / Urlaub, H. / Luhrmann, R. / Pena, V.
History
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor CWC2
B: Pre-mRNA-splicing factor CWC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2186
Polymers52,0412
Non-polymers1774
Water3,171176
1
A: Pre-mRNA-splicing factor CWC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1093
Polymers26,0211
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pre-mRNA-splicing factor CWC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1093
Polymers26,0211
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.700, 79.700, 113.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pre-mRNA-splicing factor CWC2 / PRP19-associated complex protein 40


Mass: 26020.648 Da / Num. of mol.: 2 / Fragment: UNP residues 1-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CWC2, NTC40, SLC3, YDL209C, D1041 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q12046
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG5000 MME, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNumber: 296168 / Rmerge(I) obs: 0.082 / D res high: 2.3 Å / Num. obs: 43486 / % possible obs: 96
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1047.2654599.810.043
610200010010.045
56186510010.053
45421610010.05
341178710010.069
2.531486710010.182
2.452.5217710010.371
2.42.45243610010.386
2.352.4253810010.506
2.32.35105536.710.573
ReflectionResolution: 2.2→47.264 Å / Num. obs: 27711 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.026 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.30.4275.5124766322594.2
2.3-2.40.35829460288099.9
2.4-2.50.26910.62269132423100
2.5-30.15216.61882477945100
3-40.06332.55698566385100
4-50.04940.94248062315100
5-60.05239.51108641032100
6-100.04940.98117721163100
100.04242.53300934398.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.26 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.678 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1077 5 %RANDOM
Rwork0.2214 ---
obs0.2231 21530 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57 Å2 / Biso mean: 28.256 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 4 176 3646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223548
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9454772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.875430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17923.693176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6611526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212724
X-RAY DIFFRACTIONr_mcbond_it0.4141.52141
X-RAY DIFFRACTIONr_mcangle_it0.79623416
X-RAY DIFFRACTIONr_scbond_it1.0631407
X-RAY DIFFRACTIONr_scangle_it1.8524.51356
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 79 -
Rwork0.224 1495 -
all-1574 -
obs--100 %
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)
11.5206-0.0350.11790.93250.14782.3978-0.0532-0.04230.0684-0.1399-0.03040.05980.12080.02960.08360.03410.0033-0.0160.06030.00730.062344.89741.12520.488
21.62540.18380.62281.22410.20472.5706-0.15450.2237-0.04150.09720.0582-0.0514-0.05960.10170.09630.0316-0.03580.01260.1052-0.02550.062715.85741.92846.234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 227
2X-RAY DIFFRACTION2B3 - 227

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