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- PDB-5m8c: Spliceosome component -

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Basic information

Entry
Database: PDB / ID: 5m8c
TitleSpliceosome component
ComponentsPre-mRNA-processing factor 19
KeywordsSPLICING / Spliceosome
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / Prp19 complex / U2-type catalytic step 1 spliceosome / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / protein K63-linked ubiquitination / Dual incision in TC-NER / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity ...generation of catalytic spliceosome for first transesterification step / Prp19 complex / U2-type catalytic step 1 spliceosome / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / protein K63-linked ubiquitination / Dual incision 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 / cytoplasm / cytosol
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
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 1.3Jan 17, 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

Downloads & links

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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
Water3,729207
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
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
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 / RING-type E3 ubiquitin transferase PRP19


Mass: 40688.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP19, PSO4, YLL036C / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32523, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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, hanging drop / pH: 7 / Details: 0.1 M MOPS pH 7.0 12% PEG 4000

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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: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.992 Å / Num. obs: 31956 / % possible obs: 99.3 % / Redundancy: 3.373 % / Rmerge F obs: 0.118 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.082 / Χ2: 0.932 / Net I/σ(I): 12.35 / Num. measured all: 107782 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.43.3570.490.3763.0412701382337840.44899
2.4-2.53.2310.420.3223.5810422326032260.38799
2.5-2.63.3770.3250.2614.539226275527320.30999.2
2.6-2.73.4920.2440.215.778261238823660.24899.1
2.7-2.83.4920.2090.1796.777099204920330.21199.2
2.8-33.440.1540.1388.3211344331532980.16399.5
3-43.3820.0680.06416.0728329841283770.07699.6
4-53.2420.0330.03625.959649298729760.04399.6
5-63.5150.030.03627.184643132713210.04299.5
6-103.2720.0290.03328.044699144414360.03999.4
10-48.9923.4620.0170.02340.114094164070.02797.8

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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: 3LRV

3lrv


Resolution: 2.3→48.992 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1988 6.22 %
Rwork0.1769 29965 -
obs0.1805 31953 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.4 Å2 / Biso mean: 45.4473 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 2.3→48.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5519 0 0 207 5726
Biso mean---41.47 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085626
X-RAY DIFFRACTIONf_angle_d0.8767624
X-RAY DIFFRACTIONf_chiral_restr0.056860
X-RAY DIFFRACTIONf_plane_restr0.005973
X-RAY DIFFRACTIONf_dihedral_angle_d4.5293377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35760.29321410.22692097223899
2.3576-2.42130.3041390.22812166230599
2.4213-2.49250.31551400.22492100224099
2.4925-2.5730.32161360.24992144228099
2.573-2.6650.32581410.22262131227299
2.665-2.77160.31151470.20482106225399
2.7716-2.89780.25221480.20492126227499
2.8978-3.05050.30251370.205421432280100
3.0505-3.24160.26551450.201921492294100
3.2416-3.49180.20451390.179221502289100
3.4918-3.84310.21461390.161321602299100
3.8431-4.39890.2081420.143321542296100
4.3989-5.5410.17161480.126621522300100
5.541-49.0030.19531460.16212187233399
Refinement TLS params.Method: refined / Origin x: 68.9064 Å / Origin y: 12.8411 Å / Origin z: 46.1817 Å
111213212223313233
T0.1618 Å2-0.0021 Å20.0185 Å2-0.1778 Å2-0.0173 Å2--0.1284 Å2
L0.3687 °2-0.0068 °20.2151 °2-0.5246 °2-0.4629 °2--0.4069 °2
S0.04 Å °-0.0992 Å °0.0834 Å °-0.0262 Å °-0.0767 Å °-0.0052 Å °0.0139 Å °0.0343 Å °-0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA144 - 503
2X-RAY DIFFRACTION1allB144 - 503
3X-RAY DIFFRACTION1allS1 - 207

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