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- PDB-3u1m: Structure of the mRNA splicing complex component Cwc2 -

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Basic information

Entry
Database: PDB / ID: 3u1m
TitleStructure of the mRNA splicing complex component Cwc2
ComponentsPre-mRNA-splicing factor CWC2
KeywordsSPLICING / CSMP / Zinc Finger / mRNA splicing
Function / homology
Function and homology information


pre-mRNA binding / U2-type catalytic step 1 spliceosome / Prp19 complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / positive regulation of cell cycle / positive regulation of RNA splicing / mRNA splicing, via spliceosome ...pre-mRNA binding / U2-type catalytic step 1 spliceosome / Prp19 complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLu, P. / Lu, G. / Yan, C. / Wang, L. / Li, W. / Yin, P.
CitationJournal: Biochem.J. / Year: 2012
Title: Structure of the mRNA splicing complex component Cwc2: insights into RNA recognition
Authors: Lu, P. / Lu, G. / Yan, C. / Wang, L. / Li, W. / Yin, P.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,4392
Polymers27,3731
Non-polymers651
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.719, 54.340, 111.381
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 Pre-mRNA-splicing factor CWC2 / mRNA splicing complex component Cwc2 / Complexed with CEF1 protein 2 / PRP19-associated complex ...mRNA splicing complex component Cwc2 / Complexed with CEF1 protein 2 / PRP19-associated complex protein 40 / Synthetic lethal with CLF1 protein 3


Mass: 27373.102 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CWC2, NTC40, SLC3, YDL209C, D1041 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12046
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, 21% PEG 3350, 200mM (NH4)2HCitrate, 100mM Na3Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 13, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 20560 / Num. obs: 20478 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.38 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1L

3u1l


Resolution: 1.95→29.347 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.9011 / SU ML: 0.18 / σ(F): 13.46 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1038 5.13 %RANDOM
Rwork0.159 ---
all0.1606 20478 --
obs0.1606 20239 98.72 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.172 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 84.02 Å2 / Biso mean: 20.5753 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.6014 Å20 Å2-0 Å2
2--2.3769 Å20 Å2
3----3.9783 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 1 326 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111818
X-RAY DIFFRACTIONf_angle_d1.0812445
X-RAY DIFFRACTIONf_dihedral_angle_d13.128675
X-RAY DIFFRACTIONf_chiral_restr0.086249
X-RAY DIFFRACTIONf_plane_restr0.005319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.949-2.05180.21441430.1656262297
2.0518-2.18030.17621500.14312729100
2.1803-2.34850.18651330.1466274299
2.3485-2.58480.181440.1596270098
2.5848-2.95850.18851510.1612270498
2.9585-3.72620.17961670.1541278499
3.7262-29.34990.21051500.1696292099
Refinement TLS params.Method: refined / Origin x: 20.7648 Å / Origin y: 34.612 Å / Origin z: 41.3055 Å
111213212223313233
T0.0779 Å20.0113 Å2-0.0056 Å2-0.091 Å2-0.0064 Å2--0.0831 Å2
L0.1358 °20.1238 °2-0.1575 °2-0.2904 °20.0207 °2--0.3461 °2
S-0.0092 Å °0.0246 Å °-0.0167 Å °-0.0143 Å °0.0032 Å °-0.0001 Å °-0.0036 Å °-0.0509 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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