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- PDB-2n3l: Solution structure of RNA recognition motif-1 of Plasmodium falci... -

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Basic information

Entry
Database: PDB / ID: 2n3l
TitleSolution structure of RNA recognition motif-1 of Plasmodium falciparum serine/arginine-rich protein 1.
Componentsserine/arginine-rich protein 1, PfSR1-RRM1
KeywordsRNA BINDING PROTEIN / RNA recognition motif / serine/arginine-rich protein 1
Function / homology
Function and homology information


RNA splicing / spliceosomal complex / mRNA processing / ribonucleoprotein complex / mRNA binding / nucleus / cytoplasm
Similarity search - Function
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 speciesPlasmodium falciparum 3D7 (eukaryote)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailsclosest to the average, model5
AuthorsGanguly, A. / Verma, G. / Bhavesh, N.S.
CitationJournal: J. Mol. Biol. / Year: 2019
Title: The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition.
Authors: Ganguly, A.K. / Verma, G. / Bhavesh, N.S.
History
DepositionJun 5, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
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 / _citation_author.name / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine/arginine-rich protein 1, PfSR1-RRM1


Theoretical massNumber of molelcules
Total (without water)9,9971
Polymers9,9971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein serine/arginine-rich protein 1, PfSR1-RRM1


Mass: 9997.198 Da / Num. of mol.: 1 / Fragment: RNA recognition motif-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: PFE0865c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Codonplus / References: UniProt: Q8I3T5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aromatic
11113D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] PfSR1-RRM1, 25 mM sodium phosphate, 100 mM sodium chloride, 3 mM TCEP, 50 mM L-arginine, 25 mM L-glutamate, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] PfSR1-RRM1, 25 mM sodium phosphate, 100 mM sodium chloride, 3 mM TCEP, 50 mM L-arginine, 25 mM L-glutamate, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPfSR1-RRM1-1[U-100% 13C; U-100% 15N]0.5-11
25 mMsodium phosphate-21
100 mMsodium chloride-31
3 mMTCEP-41
50 mML-arginine-51
25 mML-glutamate-61
mMPfSR1-RRM1-7[U-100% 13C; U-100% 15N]0.5-12
25 mMsodium phosphate-82
100 mMsodium chloride-92
3 mMTCEP-102
50 mML-arginine-112
25 mML-glutamate-122
Sample conditionsIonic strength: 125 / pH: 5.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANArefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1 / Details: Refinement in explicit water
NMR constraintsNOE constraints total: 803 / NOE intraresidue total count: 203 / NOE long range total count: 167 / NOE medium range total count: 135 / NOE sequential total count: 298 / Hydrogen bond constraints total count: 96
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 5

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