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- PDB-4zb4: Spliceosome component -

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Basic information

Entry
Database: PDB / ID: 4zb4
TitleSpliceosome component
ComponentsPre-mRNA-processing factor 19
KeywordsSPLICING / Spliceosome / ligase
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / U2-type catalytic step 1 spliceosome / Prp19 complex / Dual incision in TC-NER / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...generation of catalytic spliceosome for first transesterification step / U2-type catalytic step 1 spliceosome / Prp19 complex / Dual incision in TC-NER / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRocha de Moura, T. / Pena, P.
CitationJournal: To Be Published
Title: Spliceosome component
Authors: Rocha de Moura, T. / Pena, P.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-processing factor 19
B: Pre-mRNA-processing factor 19


Theoretical massNumber of molelcules
Total (without water)81,3772
Polymers81,3772
Non-polymers00
Water2,360131
1
A: Pre-mRNA-processing factor 19


Theoretical massNumber of molelcules
Total (without water)40,6891
Polymers40,6891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing factor 19


Theoretical massNumber of molelcules
Total (without water)40,6891
Polymers40,6891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.220, 100.140, 65.340
Angle α, β, γ (deg.)90.000, 92.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pre-mRNA-processing factor 19 / WD40


Mass: 40688.684 Da / Num. of mol.: 2 / Fragment: UNP residues 144-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PRP19, PSO4, YLL036C / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32523, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 32176 / Num. obs: 31956 / % possible obs: 99.3 % / Redundancy: 8.2 % / Net I/σ(I): 12.35
Reflection shellResolution: 2.331→2.396 Å / Rmerge(I) obs: 0.49

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LRV

3lrv


Resolution: 2.3→48.992 Å / FOM work R set: 0.8041 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1626 5.09 %Random selection
Rwork0.1955 30328 --
obs0.1978 31954 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.05 Å2 / Biso mean: 48.04 Å2 / Biso min: 19.01 Å2
Refinement stepCycle: final / Resolution: 2.3→48.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 0 131 5665
Biso mean---39.44 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045643
X-RAY DIFFRACTIONf_angle_d1.2017649
X-RAY DIFFRACTIONf_chiral_restr0.043862
X-RAY DIFFRACTIONf_plane_restr0.01977
X-RAY DIFFRACTIONf_dihedral_angle_d13.3252068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36770.3141330.25392490262399
2.3677-2.44410.28961210.2512550267199
2.4441-2.53150.33171350.25632471260699
2.5315-2.63280.31261250.25125392664100
2.6328-2.75270.27751360.23772510264699
2.7527-2.89780.27061280.2342524265299
2.8978-3.07930.28781310.225225332664100
3.0793-3.3170.25431190.224925642683100
3.317-3.65070.25241550.186925042659100
3.6507-4.17870.21361500.171225212671100
4.1787-5.26380.19781390.137425512690100
5.2638-49.0030.18151540.17152571272599

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