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- PDB-3lrv: The Prp19 WD40 Domain Contains a Conserved Protein Interaction Re... -

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Basic information

Entry
Database: PDB / ID: 3lrv
TitleThe Prp19 WD40 Domain Contains a Conserved Protein Interaction Region Essential for its Function.
ComponentsPre-mRNA-splicing factor 19
KeywordsSPLICING / Prp19 / WD40 / E3 ubiquitin ligase / spliceosome / DNA damage / DNA repair / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / WD repeat
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 / MAD / Resolution: 2.6 Å
AuthorsVander Kooi, C.W. / Chazin, W.J.
CitationJournal: Structure / Year: 2010
Title: The Prp19 WD40 domain contains a conserved protein interaction region essential for its function.
Authors: Vander Kooi, C.W. / Ren, L. / Xu, P. / Ohi, M.D. / Gould, K.L. / Chazin, W.J.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0274
Polymers38,7391
Non-polymers2883
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pre-mRNA-splicing factor 19
hetero molecules

A: Pre-mRNA-splicing factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0538
Polymers77,4772
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2770 Å2
ΔGint-90 kcal/mol
Surface area29670 Å2
MethodPISA
3
A: Pre-mRNA-splicing factor 19
hetero molecules

A: Pre-mRNA-splicing factor 19
hetero molecules

A: Pre-mRNA-splicing factor 19
hetero molecules

A: Pre-mRNA-splicing factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,10716
Polymers154,9544
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area8030 Å2
ΔGint-193 kcal/mol
Surface area56840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.110, 83.110, 126.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

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Components

#1: Protein Pre-mRNA-splicing factor 19


Mass: 38738.504 Da / Num. of mol.: 1 / Fragment: WD40 domain, residues 165-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP19, PSO4, YLL036C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P32523
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 2.0 M ammonium sulfate and 0.1 M Tris at pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONCAMD GCPCC11.381
SYNCHROTRONCAMD GCPCC20.9797, 0.9793, 0.9465
Detector
TypeIDDetector
MAR CCD 165 mm1CCD
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.3811
20.97971
30.97931
40.94651
ReflectionResolution: 2.6→31 Å / Num. obs: 14158 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0053refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→23.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.637 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 712 5 %RANDOM
Rwork0.22 ---
obs0.222 13408 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 15 65 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222622
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9663561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84125.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01515447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.168159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211967
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.51604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90222604
X-RAY DIFFRACTIONr_scbond_it1.39431018
X-RAY DIFFRACTIONr_scangle_it2.2534.5957
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 56 -
Rwork0.298 962 -
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)
12.7604-4.07260.558411.31912.50372.58990.01180.22960.4080.1526-0.2218-0.06120.0487-0.01720.21010.2463-0.07090.0750.42150.04950.238929.85239.8638.994
22.6067-0.67471.991111.44810.78812.43390.1563-0.07540.44570.3605-0.2351-0.79760.12460.17290.07870.30060.00080.00670.53920.0050.169636.17932.93143.213
33.6557-0.5569-0.04842.0521-0.69572.29190.23860.0325-0.16-0.5451-0.2551-0.29330.09290.14510.01650.38630.02250.02640.5957-0.03270.084439.31532.40242.796
410.0962.93182.99494.80540.4153.4509-0.1448-0.3187-0.22440.098-0.158-0.50040.08660.46060.30280.26710.07190.0030.44820.07930.093538.38621.95248.708
512.37312.0661.70987.68230.93565.65850.1609-0.469-0.41860.0858-0.0395-0.37940.14260.1309-0.12140.21810.0024-0.00450.32760.04720.031428.34617.09848.985
610.49921.21323.81354.56821.66777.54490.0364-0.6991-0.71250.1968-0.13440.06930.30630.06020.09790.32350.01950.02910.34580.09630.074824.0215.48753.637
74.6202-2.15910.20513.8608-2.66682.3276-0.0860.03060.055-0.04540.22380.12560.0887-0.2208-0.13770.4034-0.047-0.0380.46910.00990.011415.63624.16547.619
85.8156-2.1161-0.0667.6822-2.35674.66220.0829-0.0364-0.2374-0.06610.22760.24530.0971-0.4388-0.31050.3389-0.0576-0.0370.52550.00010.035111.30326.8947.092
96.66060.9401-2.30525.0303-1.45573.5724-0.11370.22570.3995-0.31640.10460.07640.0215-0.27890.0090.28060.0129-0.07830.42930.02210.058710.21436.03541.276
1011.1801-3.0406-7.51341.96161.26929.0995-0.0951-0.02550.0964-0.0504-0.09560.04030.19080.09950.19070.2332-0.0454-0.0350.26340.0610.105214.52846.50535.161
1111.2581.6004-4.2641.6564-0.14045.63810.02390.17161.0037-0.462-0.03420.0445-0.50520.47840.01040.71210.0797-0.13120.64630.10940.324719.30746.20531.056
128.4118-0.3778-0.68258.6445-0.44978.3206-0.2598-0.28530.2346-0.6224-0.07470.5696-0.13680.5370.33440.43460.04010.00660.73210.10470.226228.43542.31336.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A173 - 199
2X-RAY DIFFRACTION2A200 - 222
3X-RAY DIFFRACTION3A223 - 244
4X-RAY DIFFRACTION4A245 - 278
5X-RAY DIFFRACTION5A279 - 295
6X-RAY DIFFRACTION6A299 - 332
7X-RAY DIFFRACTION7A333 - 357
8X-RAY DIFFRACTION8A358 - 388
9X-RAY DIFFRACTION9A389 - 434
10X-RAY DIFFRACTION10A435 - 455
11X-RAY DIFFRACTION11A456 - 475
12X-RAY DIFFRACTION12A476 - 503

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