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- PDB-5m88: Spliceosome component -

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Basic information

Entry
Database: PDB / ID: 5m88
TitleSpliceosome component
ComponentsCore
KeywordsSPLICING / Spliceosome
Function / homology
Function and homology information


Prp19 complex / protein K63-linked ubiquitination / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin protein ligase activity / DNA repair
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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat ...Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoura, T.R. / Pena, V.
CitationJournal: Mol. Cell / Year: 2018
Title: Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors.
Authors: de Moura, T.R. / Mozaffari-Jovin, S. / Szabo, C.Z.K. / Schmitzova, J. / Dybkov, O. / Cretu, C. / Kachala, M. / Svergun, D. / Urlaub, H. / Luhrmann, R. / Pena, V.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core
B: Core


Theoretical massNumber of molelcules
Total (without water)31,1462
Polymers31,1462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.867, 103.013, 94.105
Angle α, β, γ (deg.)90.000, 92.590, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 70 through 133)
21(chain B and resid 70 through 133)
12(chain A and resid 1 through 55)
22(chain B and resid 1 through 55)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 70 through 133)A70 - 133
211(chain B and resid 70 through 133)B70 - 133
112(chain A and resid 1 through 55)A1 - 55
212(chain B and resid 1 through 55)B1 - 55

NCS ensembles :
ID
1
2

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Components

#1: Protein Core


Mass: 15572.780 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0072540 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SFY0

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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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5 0.4 M KCl 45% Pentaerythritol Proxalate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→47 Å / Num. obs: 13027 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 55.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Net I/σ(I): 11.1 / Num. measured all: 65996
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.54-2.6651.783771815310.7380.8681.99196
8.81-474.70.03615853340.9990.0180.0436.899.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house model

Resolution: 2.8→47.005 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 436 4.88 %RANDOM
Rwork0.25 8492 --
obs0.2517 8928 90.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.11 Å2 / Biso mean: 70.2094 Å2 / Biso min: 15.22 Å2
Refinement stepCycle: final / Resolution: 2.8→47.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 0 0 1942
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031968
X-RAY DIFFRACTIONf_angle_d0.5372668
X-RAY DIFFRACTIONf_chiral_restr0.035320
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d11.0171232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A606X-RAY DIFFRACTION8.692TORSIONAL
12B606X-RAY DIFFRACTION8.692TORSIONAL
21A539X-RAY DIFFRACTION8.692TORSIONAL
22B539X-RAY DIFFRACTION8.692TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8004-3.20560.34221140.28952287240174
3.2056-4.03840.32061580.26383058321698
4.0384-47.01110.24831640.232631473311100
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)
13.2862-3.39112.31225.1272-0.98812.82770.15980.64770.6377-0.3702-0.3873-0.6067-0.14360.49530.29560.36040.3621-0.04570.39090.22850.5658-1.2594-0.520231.5427
20.40320.5411-0.26530.6325-0.52221.1463-0.22740.47310.024-0.53140.1324-0.08380.00750.2007-0.0790.60740.09160.20080.68180.13790.33458.6007-18.4139.4255
32.7033-1.7649-1.02033.04050.09120.64080.18290.4057-0.203-0.2526-0.19130.17180.0697-0.10270.02730.33810.4539-0.06040.3794-0.17760.55734.3225-37.317629.7362
40.60980.3-0.48590.42240.64563.0564-0.25820.31020.0829-0.04420.2522-0.1887-0.40740.0989-0.08640.73340.38220.10640.64570.02670.24526.3469-14.35129.4833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )A1 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 134 )A69 - 134
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 55 )B1 - 55
4X-RAY DIFFRACTION4chain 'B' and (resid 69 through 133 )B69 - 133

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