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- PDB-2my1: Solution structure of Bud31p -

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Basic information

Entry
Database: PDB / ID: 2my1
TitleSolution structure of Bud31p
ComponentsPre-mRNA-splicing factor BUD31
KeywordsSPLICING / zinc cluster / splicing protein / zinc finger
Function / homology
Function and homology information


cellular bud site selection / U2 snRNP / spliceosomal complex / mRNA splicing, via spliceosome / nucleus
Similarity search - Function
BUD31/G10-related, conserved site / G10 protein signature 1. / G10 protein signature 2. / G10 protein / Pre-mRNA-splicing factor BUD31
Similarity search - Domain/homology
Pre-mRNA-splicing factor BUD31
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
Authorsvan Roon, A.M. / Yang, J. / Mathieu, D. / Bermel, W. / Nagai, K. / Neuhaus, D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: (113) Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p.
Authors: van Roon, A.M. / Yang, J.C. / Mathieu, D. / Bermel, W. / Nagai, K. / Neuhaus, D.
History
DepositionJan 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor BUD31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7514
Polymers18,5541
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pre-mRNA-splicing factor BUD31 / Bud site selection protein 31 / Complexed with CEF1 protein 14


Mass: 18554.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Description: Protein was expressed as an N-Terminal Glutathione S Transferase Fusion Protein
Gene: BUD31, CWC14, YCR063W, YCR63W, YCR903 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL CodonPlus / References: UniProt: P25337
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic (constant-time)
1412D 1H-13C HSQC aromatic (constant-time)
1512D 1H-15N HSQC
1612D 1H-1H NOESY
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HBHANH
11013D HBHA(CO)NH
11113D (H)CCH-COSY
11213D (H)CCH-TOCSY
11313D (H)CCH-TOCSY
11413D HNHB
11523D HACAHB
11613D 1H-15N NOESY (50ms mixing)
11713D 1H-13C NOESY aliphatic (50ms mixing)
11813D 1H-13C NOESY aromatic (50ms mixing)
11913D 1H-15N NOESY (150ms mixing)
12013D 1H-13C NOESY aliphatic (150ms mixing)
12113D 1H-13C NOESY aromatic (150ms mixing)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5 mM [U-98% 13C; U-98% 15N] Bud31p (Zn)3, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM [U-2H] DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.3-0.5 mM [U-98% 13C; U-98% 15N] Bud31p (Zn)3, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM [U-2H] DTT, 100% D2O100% D2O
30.3-0.5 mM [U-98% 15N] Bud31p (Zn)3, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM [U-2H] DTT, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMBud31p (Zn)3-1[U-98% 13C; U-98% 15N]0.3-0.51
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-4[U-2H]1
mMBud31p (Zn)3-5[U-98% 13C; U-98% 15N]0.3-0.52
20 mMsodium phosphate-62
150 mMsodium chloride-72
1 mMDTT-8[U-2H]2
mMBud31p (Zn)3-9[U-98% 15N]0.3-0.53
20 mMsodium phosphate-103
150 mMsodium chloride-113
1 mMDTT-12[U-2H]3
Sample conditionsIonic strength: 0.27 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance AVIBrukerAvance AVI8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospinprocessing
Sparky3.115Goddardchemical shift assignment
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1828 / NOE intraresidue total count: 676 / NOE long range total count: 354 / NOE medium range total count: 390 / NOE sequential total count: 408 / Hydrogen bond constraints total count: 30 / Protein chi angle constraints total count: 57 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 35 / Maximum torsion angle constraint violation: 5.85 ° / Maximum upper distance constraint violation: 0.322 Å

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