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- PDB-2m7s: NMR structure of RNA recognition motif 2 (RRM2) of Homo sapiens s... -

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Basic information

Entry
Database: PDB / ID: 2m7s
TitleNMR structure of RNA recognition motif 2 (RRM2) of Homo sapiens splicing factor, arginine/serine-rich 1
ComponentsSerine/arginine-rich splicing factor 1
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


protein localization to P-body / DNA topoisomerase binding / RS domain binding / protein kinase B binding / interleukin-17-mediated signaling pathway / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / mRNA stabilization / Transport of Mature mRNA derived from an Intron-Containing Transcript ...protein localization to P-body / DNA topoisomerase binding / RS domain binding / protein kinase B binding / interleukin-17-mediated signaling pathway / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / mRNA stabilization / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / signal transduction involved in regulation of gene expression / regulation of RNA splicing / mRNA 5'-splice site recognition / mRNA Splicing - Minor Pathway / oligodendrocyte differentiation / Processing of Capped Intron-Containing Pre-mRNA / protein localization to nucleus / mRNA transport / cardiac muscle contraction / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / liver regeneration / mRNA splicing, via spliceosome / mRNA processing / nuclear envelope / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / SRSF1, RNA recognition motif 1 / : / RRM (RNA recognition motif) 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 ...: / SRSF1, RNA recognition motif 1 / : / RRM (RNA recognition motif) 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/arginine-rich splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model13
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of RNA recognition motif 2 (RRM2) of Homo sapiens splicing factor, arginine/serine-rich 1
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionApr 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 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: Serine/arginine-rich splicing factor 1


Theoretical massNumber of molelcules
Total (without water)10,2071
Polymers10,2071
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Serine/arginine-rich splicing factor 1 / Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine-rich 1 / pre-mRNA- ...Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine-rich 1 / pre-mRNA-splicing factor SF2 / P33 subunit


Mass: 10207.403 Da / Num. of mol.: 1 / Fragment: UNP residues 106-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRSF1, ASF, SF2, SF2P33, SFRS1, OK/SW-cl.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q07955

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of RNA recognition motif 2 (RRM2) of Homo sapiens splicing factor, arginine/serine-rich 1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1214D-HACANH-APSY
1315D-CBCA(CO)NH-APSY
1415D-(HA)CA(CO)NH-APSY
1513D 1H-13C NOESY aliphatic with non-uniform sampling
1613D 1H-13C NOESY aromatic with non-uniform sampling
1713D 1H-15N NOESY with non-uniform sampling

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-99% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.0798 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
j-UNIOHerrmann, Guntert and Wuthrichchemical shift assignment
j-UNIOHerrmann, Guntert and Wuthrichpeak picking
j-UNIOHerrmann, Guntert and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
TopSpin3.1Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1414 / NOE intraresidue total count: 317 / NOE long range total count: 479 / NOE medium range total count: 204 / NOE sequential total count: 394
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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