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- PDB-1zkh: Solution structure of a human ubiquitin-like domain in SF3A1 -

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Basic information

Entry
Database: PDB / ID: 1zkh
TitleSolution structure of a human ubiquitin-like domain in SF3A1
ComponentsSplicing factor 3 subunit 1
KeywordsGENE REGULATION / UBIQUITIN / SPLICING FACTOR / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex ...mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Splicing factor 3A subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / 100 structures were calculated by CYANA 2.0 using 2667 NOE-derived distance constraints, 121 dihedral angle constraints, and 50 distance constraints from hydrogen bonds. The 20 structures with lowest target functions were subjected to refinement with CNS 1.1.
AuthorsLukin, J.A. / Dhe-Paganon, S. / Guido, V. / Lemak, A. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Edwards, A. ...Lukin, J.A. / Dhe-Paganon, S. / Guido, V. / Lemak, A. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Solution structure of a human ubiquitin-like domain in SF3A1
Authors: Lukin, J.A. / Dhe-Paganon, S. / Guido, V. / Lemak, A. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C.H.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 3 subunit 1


Theoretical massNumber of molelcules
Total (without water)9,5651
Polymers9,5651
Non-polymers00
Water0
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 #11closest to the average

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Components

#1: Protein Splicing factor 3 subunit 1 / / Spliceosome associated protein 114 / SAP 114 / SF3a120 / SF3A1


Mass: 9565.140 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3A1, SAP114 / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B21 (DE3) GOLD MAGIC / References: UniProt: Q15459

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM protein, U-15N, U-13C; 300 mM NaCl, 1mM benzamidine, 10mM DTT, 0.01% NaN3, 10mM Sodium Acetate, 0.01mM ZnSO4, 90%H2O, 10%D2O90% H2O/10% D2O
22mM protein, U-15N, U-13C; 300 mM NaCl, 1mM benzamidine, 10mM DTT, 0.01% NaN3, 10mM Sodium Acetate, 0.01mM ZnSO4, 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 300 mM NaCl / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospin, Inc.collection
NMRPipe2.1Delaglio, F.processing
CYANA2Guentert, P. et al.structure solution
CNS1.1Brunger, A. et al.refinement
RefinementMethod: 100 structures were calculated by CYANA 2.0 using 2667 NOE-derived distance constraints, 121 dihedral angle constraints, and 50 distance constraints from hydrogen bonds. The 20 structures ...Method: 100 structures were calculated by CYANA 2.0 using 2667 NOE-derived distance constraints, 121 dihedral angle constraints, and 50 distance constraints from hydrogen bonds. The 20 structures with lowest target functions were subjected to refinement with CNS 1.1.
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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