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- PDB-2dt7: Solution structure of the second SURP domain of human splicing fa... -

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Basic information

Entry
Database: PDB / ID: 2dt7
TitleSolution structure of the second SURP domain of human splicing factor SF3a120 in complex with a fragment of human splicing factor SF3a60
Components
  • Splicing factor 3 subunit 1
  • Splicing factor 3A subunit 3
KeywordsRNA BINDING PROTEIN / structure genomics / SF3a120 / SF3a60 / SURP domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway ...RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / 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 / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Surp module / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Splicing factor 3A subunit 1, ubiquitin domain / : / Replication stress response SDE2 C-terminal / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 ...Surp module / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Splicing factor 3A subunit 1, ubiquitin domain / : / Replication stress response SDE2 C-terminal / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / : / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Splicing factor 3A subunit 3 / Splicing factor 3A subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, restrained ENERGY MINIMIZATION
AuthorsHe, F. / Kuwasako, K. / Inoue, M. / Guntert, P. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2006
Title: Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP
Authors: Kuwasako, K. / He, F. / Inoue, M. / Tanaka, A. / Sugano, S. / Guentert, P. / Muto, Y. / Yokoyama, S.
History
DepositionJul 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 3A subunit 3
B: Splicing factor 3 subunit 1


Theoretical massNumber of molelcules
Total (without water)14,4422
Polymers14,4422
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 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Splicing factor 3A subunit 3 / Spliceosome-associated protein 61 / SAP 61 / SF3a60


Mass: 4452.058 Da / Num. of mol.: 1 / Fragment: residues 70-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3a60, SF3a3
Plasmid: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SURP2 (134-217)
Production host: Escherichia coli (E. coli) / References: UniProt: Q12874
#2: Protein Splicing factor 3 subunit 1 / Spliceosome-associated protein 114 / SAP 114 / SF3a120


Mass: 9990.318 Da / Num. of mol.: 1 / Fragment: SURP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3a120/SF3a1
Plasmid: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SURP2 (134-217)
Production host: Escherichia coli (E. coli) / 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

DetailsContents: 2.0mM U-15N, 13C PROTEIN; 20mM sodium phosphate; 1mM d-DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM / pH: 6 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9321Kobayashi, N.data analysis
CYANA2.1Guntert, P.structure solution
OPALp1.4Koradi, R.structure solution
CYANA2.1Guntert, P.refinement
OPALp1.4Koradi, R.refinement
RefinementMethod: TORSION ANGLE DYNAMICS, restrained ENERGY MINIMIZATION
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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