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- PDB-7vh9: Solution structure of the chimeric peptide of the first SURP doma... -

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Basic information

Entry
Database: PDB / ID: 7vh9
TitleSolution structure of the chimeric peptide of the first SURP domain of Human SF3A1 and the interacting region of SF1.
ComponentsSplicing factor 3A subunit 1,Splicing factor 1
KeywordsSPLICING / SURP / U2 snRNP / SF3A1 / SF1
Function / homology
Function and homology information


U2AF complex / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition ...U2AF complex / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / negative regulation of smooth muscle cell proliferation / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear speck / ribosome / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Splicing factor 3A subunit 1, ubiquitin domain / 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 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Splicing factor 3A subunit 1 / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMuto, Y. / Kuwasako, K. / Takizawa, M. / Kobayashi, N. / Sakamoto, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15K06982 Japan
The Sumitomo Foundation151227 Japan
The Takeda Science Foundation Japan
CitationJournal: Protein Sci. / Year: 2022
Title: Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.
Authors: Nameki, N. / Takizawa, M. / Suzuki, T. / Tani, S. / Kobayashi, N. / Sakamoto, T. / Muto, Y. / Kuwasako, K.
History
DepositionSep 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: 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: Splicing factor 3A subunit 1,Splicing factor 1


Theoretical massNumber of molelcules
Total (without water)12,1331
Polymers12,1331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Splicing factor 3A subunit 1,Splicing factor 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114 / Mammalian branch point-binding protein / ...SF3a120 / Spliceosome-associated protein 114 / SAP 114 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162


Mass: 12133.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3A1, SAP114, SF1, ZFM1, ZNF162 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15459, UniProt: Q15637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D 13C,15N-SEPARATED NOESY SPECTRA

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Sample preparation

DetailsType: solution
Contents: 1.4 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O
Details: 20 mM sodium phosphate buffer (pH 7.0); 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.4 mM / Component: protein / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 20 mM sodium phosphate buffer (pH 7.0); 1mM D-DTT; 0.02% NaN3
Ionic strength: 20 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
MagRO-NMRViewKobayshi, N.chemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TopSpin2.1Bruker Biospincollection
NMRPipe2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS2007Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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