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- PDB-7p08: Solution structure of the human SF3A1 ubiquitin-like domain -

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Basic information

Entry
Database: PDB / ID: 7p08
TitleSolution structure of the human SF3A1 ubiquitin-like domain
ComponentsIsoform 1 of Splicing factor 3A subunit 1
KeywordsSPLICING / Spliceosome / U2 snRNP / SF3A / ubiqutin-like domain
Function / homologyIsoform 1 of Splicing factor 3A subunit 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Authorsde Vries, T. / Campagne, S. / Allain, F.H.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Sequence-specific RNA recognition by an RGG motif connects U1 and U2 snRNP for spliceosome assembly.
Authors: de Vries, T. / Martelly, W. / Campagne, S. / Sabath, K. / Sarnowski, C.P. / Wong, J. / Leitner, A. / Jonas, S. / Sharma, S. / Allain, F.H.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 19, 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: Isoform 1 of Splicing factor 3A subunit 1


Theoretical massNumber of molelcules
Total (without water)10,2391
Polymers10,2391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform 1 of Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 10238.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3A1, SAP114 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: Q15459-1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D HN(CA)CB
121isotropic33D CBCA(CO)NH
131isotropic33D HNCO
141isotropic33D H(CCO)NH
151isotropic33D H(CCO)NH
171isotropic13D 15N-1H HSQC NOESY
181isotropic13D 13Cali-1H HSQC NOESY
191isotropic13D 13Caro-1H HSQC NOESY
1102isotropic2{1H}-15N heteronuclear NOE

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution21.1 mM [U-100% 15N] SF3A1, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMSF3A1[U-13C; U-15N]1
1.1 mMSF3A1[U-100% 15N]2
Sample conditionsDetails: 10 mM NaPO4, 50 mM sodium chloride / Ionic strength: 60 mM / Label: condition_1 / pH: 6 / Pressure: atmospheric Pa / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVIIIBrukerAVIII7002
Bruker AVANCE NEOBrukerAVANCE NEO6003

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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