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- PDB-2mhn: NMR structure of the first RRM domain of the protein RBM39 from H... -

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Basic information

Entry
Database: PDB / ID: 2mhn
TitleNMR structure of the first RRM domain of the protein RBM39 from Homo sapiens
ComponentsRNA-binding protein 39
KeywordsTRANSCRIPTION / T-Cell / PSI-Biology / RNA binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck ...RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / nucleoplasm
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
RNA-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsSerrano, P. / Geralt, M. / Dutta, S.K. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of the first RRM domain of the protein RBM39 from Homo sapiens
Authors: Serrano, P. / Wuthrich, K. / Geralt, M. / Dutta, S.K.
History
DepositionDec 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)10,5741
Polymers10,5741
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 / 80target function
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 39 / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing ...Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Splicing factor HCC1


Mass: 10574.178 Da / Num. of mol.: 1 / Fragment: RRM 1 domain residues 144-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM39, HCC1, RNPC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q14498

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
1514D APSY HACANH
1615D APSY CBCA(CO)NH
1715D APSY (HA)CA(CO)NH

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Sample preparation

DetailsContents: 0.6 mM [U-98% 13C; U-98% 15N] protein, 100 mM sodium chloride, 10 mM [U-99% 2H] sodium acetate, 5 mM sodium azide, 2 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity-1[U-98% 13C; U-98% 15N]1
100 mMsodium chloride-21
10 mMsodium acetate-3[U-99% 2H]1
5 mMsodium azide-41
2 mMDTT-51
Sample conditionsIonic strength: 0.220 / pH: 5 / 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
NameDeveloperClassification
CYANAGuntert P.refinement
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1364 / NOE intraresidue total count: 390 / NOE long range total count: 344 / NOE medium range total count: 237 / NOE sequential total count: 393
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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