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- PDB-6hpj: Structure of human SRSF1 RRM1 bound to AACAAA RNA -

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Basic information

Entry
Database: PDB / ID: 6hpj
TitleStructure of human SRSF1 RRM1 bound to AACAAA RNA
Components
  • Immunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 1
  • RNA (5'-R(*AP*AP*CP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / splicing / SR protein / SRSF1 / RRM / spinal muscular atrophy / SMA / RNA
Function / homology
Function and homology information


DNA topoisomerase binding / protein kinase B binding / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / mRNA Splicing - Minor Pathway / regulation of RNA splicing ...DNA topoisomerase binding / protein kinase B binding / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / mRNA Splicing - Minor Pathway / regulation of RNA splicing / oligodendrocyte differentiation / Processing of Capped Intron-Containing Pre-mRNA / mRNA 5'-splice site recognition / mRNA transport / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / liver regeneration / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / mRNA binding / RNA binding / extracellular region / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / SRSF1, RNA recognition motif 1 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...: / SRSF1, RNA recognition motif 1 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / Immunoglobulin G-binding protein G / Serine/arginine-rich splicing factor 1
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAllain, F.T.H. / Clery, A.
CitationJournal: Nat Commun / Year: 2021
Title: Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing.
Authors: Clery, A. / Krepl, M. / Nguyen, C.K.X. / Moursy, A. / Jorjani, H. / Katsantoni, M. / Okoniewski, M. / Mittal, N. / Zavolan, M. / Sponer, J. / Allain, F.H.
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Immunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 1
A: RNA (5'-R(*AP*AP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,8632
Polymers19,8632
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: ITC and NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1780 Å2
ΔGint0 kcal/mol
Surface area5910 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: Antibody Immunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 1 / IgG-binding protein G / Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine- ...IgG-binding protein G / Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine-rich 1 / pre-mRNA-splicing factor SF2 / P33 subunit


Mass: 17956.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GB1 tag followed by 6His tag and SRSF1 RRM1 from amino acid 1 to 97,GB1 tag followed by 6His tag and SRSF1 RRM1 from amino acid 1 to 97
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Gene: spg, SRSF1, ASF, SF2, SF2P33, SFRS1, OK/SW-cl.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P19909, UniProt: Q07955
#2: RNA chain RNA (5'-R(*AP*AP*CP*AP*AP*A)-3')


Mass: 1906.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA molecule / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic42D NOESY
122isotropic33D 1H-15N NOESY
133isotropic32D 1H-13C HSQC aliphatic
143isotropic32D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-99% 15N] SRSF1 RRM1, 0.5 mM RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 100% D2O20mM NaHPO4 pH7, 50mM Arg, 50mM Glu, 0.05% beta-mercaptoethanolsample1100% D2O
solution20.5 mM [U-99% 15N] SRSF1 RRM1, 0.5 mM NA RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 90% H2O/10% D2O20mM NaHPO4 pH7, 50mM Arg, 50mM Glu, 0.05% beta-mercaptoethanolsample290% H2O/10% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] SRSF1 RRM1, 0.5 mM NA RNA (5'-R(*AP*AP*CP*AP*AP*A)-3'), 90% H2O/10% D2O20mM NaHPO4 pH7, 50mM Arg, 50mM Glu, 0.05% beta-mercaptoethanolsample390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSRSF1 RRM1[U-99% 15N]1
0.5 mMRNA (5'-R(*AP*AP*CP*AP*AP*A)-3')natural abundance1
0.5 mMSRSF1 RRM1[U-99% 15N]2
0.5 mMRNA (5'-R(*AP*AP*CP*AP*AP*A)-3')NA2
0.5 mMSRSF1 RRM1[U-99% 13C; U-99% 15N]3
0.5 mMRNA (5'-R(*AP*AP*CP*AP*AP*A)-3')NA3
Sample conditionsDetails: 20mM NaHPO4 pH7, 50mM Arg, 50mM Glu, 0.05% beta-mercaptoethanol
Ionic strength: 120 mM / Label: sample / pH: 7 Not defined / Pressure: atmospheric atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker 500 AVIIIBruker500 AVIII5001
Bruker 600 AVIIIBruker600 AVIII6002
Bruker 700 AVIIIBruker700 AVIII7003
b 900 AVIIIb900 AVIII9004

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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