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- PDB-4lg8: Crystal structure of PRPF19 WD40 repeats -

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Basic information

Entry
Database: PDB / ID: 4lg8
TitleCrystal structure of PRPF19 WD40 repeats
ComponentsPre-mRNA-processing factor 19
KeywordsDNA BINDING PROTEIN / Structural Genomics Consortium / SGC / wd40 repeat
Function / homology
Function and homology information


Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / spliceosomal complex assembly / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / proteasomal protein catabolic process ...Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / spliceosomal complex assembly / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / proteasomal protein catabolic process / catalytic step 2 spliceosome / lipid droplet / mRNA Splicing - Major Pathway / DNA damage checkpoint signaling / spliceosomal complex / RING-type E3 ubiquitin transferase / protein localization / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / double-strand break repair via nonhomologous end joining / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / site of double-strand break / nuclear speck / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsXu, C. / Tempel, W. / He, H. / Dobrovetsky, E. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of the WD40 domain of human PRPF19.
Authors: Zhang, Y. / Li, Y. / Liang, X. / Zhu, Z. / Sun, H. / He, H. / Min, J. / Liao, S. / Liu, Y.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2May 10, 2017Group: Database references / Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Jan 3, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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-processing factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,10617
Polymers39,0601
Non-polymers4616
Water2,432135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.055, 83.055, 75.533
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / Senescence evasion factor


Mass: 39059.914 Da / Num. of mol.: 1 / Fragment: UNP residues 169-504 / Mutation: K189E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: sf9 / Gene: PRPF19, NMP200, PRP19, SNEV / Plasmid: pFBOH-MHL / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UMS4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT PROTEOLYSIS OF THE PROTEIN CONSTRUCT MAY HAVE OCCURRED

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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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG-3350, 0.2 M disodium tartrate, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→40 Å / Num. obs: 24511 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.936 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.929.90.98611811.3551100
1.92-1.969.90.89512131.3811100
1.96-2100.72412051.4911100
2-2.0410.20.63412251.4941100
2.04-2.0810.20.51112051.5431100
2.08-2.1310.20.44312141.6351100
2.13-2.1810.20.38411981.7031100
2.18-2.2410.30.31112401.831100
2.24-2.3110.30.28411901.821100
2.31-2.3810.40.25712141.8431100
2.38-2.4710.40.21612331.8851100
2.47-2.5610.50.18812061.9141100
2.56-2.6810.50.16312381.9561100
2.68-2.8210.50.11912042.0261100
2.82-310.50.10112282.1271100
3-3.2310.50.07812252.2111100
3.23-3.5610.50.05612462.2811100
3.56-4.0710.40.04812472.4891100
4.07-5.1310.30.04112692.5531100
5.13-409.60.05213302.981100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.12data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OW8, 2YMU, 2CO0

3ow8

2ymu

2co0


Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1761 / WRfactor Rwork: 0.1418 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8726 / SU B: 5.856 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1321 / SU Rfree: 0.1251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: phenix, arp/warp, coot and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 1231 5 %RANDOM
Rwork0.156 ---
obs0.1581 24457 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.5 Å2 / Biso mean: 33.7748 Å2 / Biso min: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.8 Å20 Å2
2---0.8 Å20 Å2
3---2.61 Å2
Refinement stepCycle: LAST / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 16 135 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192439
X-RAY DIFFRACTIONr_bond_other_d0.0020.022269
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9373325
X-RAY DIFFRACTIONr_angle_other_deg0.80735230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0224.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09815391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.35156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_mcbond_it1.892.141245
X-RAY DIFFRACTIONr_mcbond_other1.8842.1391244
X-RAY DIFFRACTIONr_mcangle_it2.5963.2011556
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 95 -
Rwork0.231 1649 -
all-1744 -
obs--97.81 %
Refinement TLS params.Method: refined / Origin x: 32.6593 Å / Origin y: 2.5142 Å / Origin z: 7.9443 Å
111213212223313233
T0.0626 Å20.0014 Å2-0.0058 Å2-0.0521 Å2-0.0108 Å2--0.0245 Å2
L1.5648 °2-0.5232 °2-0.1497 °2-2.0825 °2-0.0774 °2--0.572 °2
S-0.0101 Å °0.114 Å °-0.1516 Å °-0.1214 Å °-0.007 Å °0.186 Å °0.0756 Å °-0.1002 Å °0.0171 Å °

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