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- PDB-2my3: Snu17p-Pml1p structure intermediate during RES complex assembly -

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Basic information

Entry
Database: PDB / ID: 2my3
TitleSnu17p-Pml1p structure intermediate during RES complex assembly
Components
  • Pre-mRNA leakage protein 1
  • U2 snRNP component IST3
KeywordsSPLICING / spliceosome / Snu17p / Ist3p / Pml1p / heterodimer / cooperativity / RES / RRM
Function / homology
Function and homology information


RES complex / maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / generation of catalytic spliceosome for first transesterification step / miRNA processing / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly ...RES complex / maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / generation of catalytic spliceosome for first transesterification step / miRNA processing / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / mRNA export from nucleus / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Ist3-like, RNA recognition motif / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Ist3-like, RNA recognition motif / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
U2 snRNP component IST3 / Pre-mRNA leakage protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsWysoczanski, P. / Becker, S. / Zweckstetter, M.
CitationJournal: Sci Rep / Year: 2015
Title: Structures of intermediates during RES complex assembly.
Authors: Wysoczanski, P. / Becker, S. / Zweckstetter, M.
History
DepositionJan 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U2 snRNP component IST3
B: Pre-mRNA leakage protein 1


Theoretical massNumber of molelcules
Total (without water)16,0112
Polymers16,0112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein U2 snRNP component IST3 / Increased sodium tolerance protein 3 / U2 snRNP protein SNU17


Mass: 13495.979 Da / Num. of mol.: 1 / Fragment: UNP residues(25-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: IST3, SNU17, YIB5W, YIR005W / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40565
#2: Protein/peptide Pre-mRNA leakage protein 1


Mass: 2514.782 Da / Num. of mol.: 1 / Fragment: UNP residues(22-42)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: L1591, PML1, YLR016C / Plasmid: modified pET-28b with TEV cleavage site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07930

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-15N HSQC
1422D 1H-15N HSQC
1512D 1H-15N HSQC
1622D 1H-15N HSQC
1712D 1H-15N HSQC
1822D 1H-15N HSQC
1912D 1H-13C HSQC aliphatic
11013D 1H-13C NOESY aromatic
11123D 1H-13C NOESY aromatic
11223D 1H-13C NOESY aliphatic
11313D HNCO
11413D HNCA
11523D HNCA
11613D HN(CO)CA
11723D HN(CO)CA
11813D (H)CCH-TOCSY
11913D 1H-15N NOESY
12023D 1H-15N NOESY
1211(HB)CB(CGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM sodium phosphate, 250 mM sodium chloride, 0.8-1 mM [U-13C; U-15N] Snu17p, 1.2-1.5 mM Pml1p_Fmoc, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
225 mM sodium phosphate, 250 mM sodium chloride, 1-1.2 mM Snu17p, 0.8-1 mM [U-13C; U-15N] Pml1p, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
25 mMsodium phosphate-11
250 mMsodium chloride-21
mMSnu17p-3[U-13C; U-15N]0.8-11
mMPml1p_Fmoc-41.2-1.51
1 mMsodium azide-51
25 mMsodium phosphate-62
250 mMsodium chloride-72
mMSnu17p-81-1.22
mMPml1p-9[U-13C; U-15N]0.8-12
1 mMsodium azide-102
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Analysis_CCPNCCPNchemical shift assignment
TopSpinBruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2258 / NOE intraresidue total count: 558 / NOE long range total count: 856 / NOE sequential total count: 616 / Hydrogen bond constraints total count: 50 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 115
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.7 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.1 Å / Torsion angle constraint violation method: x-plor nih
NMR ensemble rmsDistance rms dev: 0.021 Å / Distance rms dev error: 0.002 Å

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