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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 / U2-type catalytic step 1 spliceosome / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin protein ligase activity / DNA repair / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats profile. ...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 / Trp-Asp (WD) repeats profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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: Tales Rocha de Moura / Sina Mozaffari-Jovin / Csaba Zoltán Kibédi Szabó / Jana Schmitzová / Olexandr Dybkov / Constantin Cretu / Michael Kachala / Dmitri Svergun / Henning Urlaub / ...Authors: Tales Rocha de Moura / Sina Mozaffari-Jovin / Csaba Zoltán Kibédi Szabó / Jana Schmitzová / Olexandr Dybkov / Constantin Cretu / Michael Kachala / Dmitri Svergun / Henning Urlaub / Reinhard Lührmann / Vladimir Pena /
Abstract: Human nineteen complex (NTC) acts as a multimeric E3 ubiquitin ligase in DNA repair and splicing. The transfer of ubiquitin is mediated by Prp19-a homotetrameric component of NTC whose elongated ...Human nineteen complex (NTC) acts as a multimeric E3 ubiquitin ligase in DNA repair and splicing. The transfer of ubiquitin is mediated by Prp19-a homotetrameric component of NTC whose elongated coiled coils serve as an assembly axis for two other proteins called SPF27 and CDC5L. We find that Prp19 is inactive on its own and have elucidated the structural basis of its autoinhibition by crystallography and mutational analysis. Formation of the NTC core by stepwise assembly of SPF27, CDC5L, and PLRG1 onto the Prp19 tetramer enables ubiquitin ligation. Protein-protein crosslinking of NTC, functional assays in vitro, and assessment of its role in DNA damage response provide mechanistic insight into the organization of the NTC core and the communication between PLRG1 and Prp19 that enables E3 activity. This reveals a unique mode of regulation for a complex E3 ligase and advances understanding of its dynamics in various cellular pathways.
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
Revision 1.3May 1, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water00
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:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARG(chain A and resid 70 through 133)AA70 - 13370 - 133
21SERSERARGARG(chain B and resid 70 through 133)BB70 - 13370 - 133
12METMETILEILE(chain A and resid 1 through 55)AA1 - 551 - 55
22METMETILEILE(chain B and resid 1 through 55)BB1 - 551 - 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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