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- PDB-4ilj: Crystal structure of an Prp8p RNaseH W1911A mutant protein -

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Basic information

Entry
Database: PDB / ID: 4ilj
TitleCrystal structure of an Prp8p RNaseH W1911A mutant protein
ComponentsPre-mRNA-splicing factor 8
KeywordsSPLICING / U5 snRNP assembly / Aar2 / Prp8
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0001 Å
AuthorsWeber, G. / Heroven, C. / Santos, K.F. / Wahl, M.C.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis for dual roles of Aar2p in U5 snRNP assembly.
Authors: Weber, G. / Cristao, V.F. / Santos, K.F. / Jovin, S.M. / Heroven, A.C. / Holton, N. / Luhrmann, R. / Beggs, J.D. / Wahl, M.C.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)58,7722
Polymers58,7722
Non-polymers00
Water6,593366
1
A: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)29,3861
Polymers29,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)29,3861
Polymers29,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.600, 85.022, 95.955
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 8


Mass: 29385.980 Da / Num. of mol.: 2 / Fragment: yPrp8 RNaseH (UNP Residues 1835-2090) / Mutation: W1911A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-Cl pH 8.5, 12% PEG 3350, 100 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 2, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 42465 / Num. obs: 42335 / % possible obs: 99.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Rsym value: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.05 Å / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.57 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EO9

3eo9


Resolution: 2.0001→37.8 Å / SU ML: 0.21 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2117 5 %RANDOM
Rwork0.1799 ---
all0.1822 42465 --
obs0.1822 42330 99.7 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0001→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 0 366 4434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014389
X-RAY DIFFRACTIONf_angle_d1.1885989
X-RAY DIFFRACTIONf_dihedral_angle_d14.4421672
X-RAY DIFFRACTIONf_chiral_restr0.081701
X-RAY DIFFRACTIONf_plane_restr0.005765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.27951380.24372622X-RAY DIFFRACTION100
2.0466-2.09780.26871400.21992646X-RAY DIFFRACTION100
2.0978-2.15450.28711390.21152648X-RAY DIFFRACTION100
2.1545-2.21790.25911390.21082643X-RAY DIFFRACTION100
2.2179-2.28950.27641400.20012657X-RAY DIFFRACTION100
2.2895-2.37130.25131400.19362651X-RAY DIFFRACTION100
2.3713-2.46620.24031390.18292653X-RAY DIFFRACTION100
2.4662-2.57840.2521420.18922680X-RAY DIFFRACTION100
2.5784-2.71440.22711410.18552682X-RAY DIFFRACTION100
2.7144-2.88440.25531390.18772638X-RAY DIFFRACTION100
2.8844-3.1070.26721420.19792696X-RAY DIFFRACTION100
3.107-3.41940.2421420.18282699X-RAY DIFFRACTION100
3.4194-3.91380.21811430.16542720X-RAY DIFFRACTION100
3.9138-4.92930.16341430.14492717X-RAY DIFFRACTION99
4.9293-37.80670.20351500.17632861X-RAY DIFFRACTION99
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)
11.5892-1.79070.49262.1402-1.25611.3716-0.0088-0.1489-0.02260.15840.00710.09610.0796-0.1775-0.01130.21680.0096-0.00480.2007-0.00410.1728-34.0122-4.242210.7926
21.1817-0.5535-0.09962.68650.12182.05880.01110.0086-0.07610.2440.00990.06690.1143-0.01640.00770.1792-0.00180.00990.20650.00370.2046-37.7993-3.25156.0382
32.5224-1.95310.65854.1162-0.25543.02870.2890.1566-0.3515-0.7437-0.2010.03720.53060.42710.02930.41770.1109-0.01970.3545-0.04530.2914-28.7265-14.0886-9.2966
42.50150.5221-0.05031.10140.48940.2487-0.410.7863-0.7917-1.392-0.17620.52030.3132-0.5591-0.03990.4599-0.08530.08920.4689-0.10510.467-16.6654-34.765110.8777
51.0419-0.176-0.49052.126-0.13751.95260.1332-0.06680.0355-0.0789-0.19830.0229-0.37780.4258-0.03610.2247-0.02210.02150.30120.03910.2131-24.0957-26.640625.3422
61.14630.6798-0.49272.1059-0.48760.93380.084-0.09250.14920.3483-0.04720.3894-0.315-0.0071-0.05760.29840.0240.06950.25460.01710.2854-29.3735-22.139933.4567
72.30261.8197-2.60532.5029-2.31333.23950.05280.20480.12940.21520.19260.6395-0.1668-0.451-0.12150.33120.0043-0.05440.33360.02860.3661-33.1637-20.856222.5842
81.0654-0.3204-0.85662.5439-0.51761.7222-0.22260.2946-0.0504-0.86490.15440.14280.332-0.0731-0.00470.364-0.0596-0.06310.30280.03480.2634-25.9712-23.286314.7137
92.1981-0.46030.32861.82380.08061.4115-0.2412-0.18-0.0838-0.58430.34410.18430.0473-0.1952-0.04110.4709-0.0844-0.06790.30710.0310.2957-26.1609-28.509513.1025
101.840.4685-0.2672.0979-0.23610.42060.173-0.37490.22270.2841-0.0682-0.1782-0.27950.2528-0.02760.2806-0.02350.030.26630.01510.2706-15.3631-19.763830.4494
112.19310.04160.66492.49020.45971.47-0.0313-0.5136-0.08750.26880.0583-0.4892-0.07520.02210.00260.12610.0054-0.02930.26080.04840.1876-6.3514-28.248331.5026
122.57381.90260.01444.79870.00991.39410.0356-0.4048-0.32050.3775-0.1249-0.88230.39310.32680.04330.35320.06040.02840.38820.07330.5121-3.173-38.410630.7505
131.1442-0.79210.31062.2077-0.89621.1537-0.26250.7018-0.2126-0.4866-0.0406-0.95261.10060.19690.06030.67690.0820.08720.52310.0460.7204-5.8487-48.735624.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1833 through 1904 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1905 through 2026 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2027 through 2086 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1833 through 1844 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1845 through 1864 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1865 through 1904 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1905 through 1923 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1924 through 1947 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1948 through 1964 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1965 through 2000 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2001 through 2044 )
12X-RAY DIFFRACTION12chain 'B' and (resid 2045 through 2067 )
13X-RAY DIFFRACTION13chain 'B' and (resid 2068 through 2086 )

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