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- PDB-2m9k: RBPMS2-Nter -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2m9k
TitleRBPMS2-Nter
ComponentsRNA-binding protein with multiple splicing 2
KeywordsRNA BINDING PROTEIN / RBPMS2
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / embryonic digestive tract morphogenesis / negative regulation of BMP signaling pathway / positive regulation of smooth muscle cell proliferation / mRNA binding / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
RBPMS2, 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 with multiple splicing 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYang, Y.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Homodimerization of RBPMS2 through a new RRM-interaction motif is necessary to control smooth muscle plasticity.
Authors: Sagnol, S. / Yang, Y. / Bessin, Y. / Allemand, F. / Hapkova, I. / Notarnicola, C. / Guichou, J.F. / Faure, S. / Labesse, G. / de Santa Barbara, P.
History
DepositionJun 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details
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

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein with multiple splicing 2
B: RNA-binding protein with multiple splicing 2


Theoretical massNumber of molelcules
Total (without water)21,0022
Polymers21,0022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1472.6 Å2
ΔGint-7.8 kcal/mol
Surface area11384.8 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein with multiple splicing 2


Mass: 10501.166 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 27-117)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBPMS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZRY4

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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-1H NOESY
1413D HNCO
1513D HNCA
1613D CBCA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.4-0.8 mM [U-100% 15N] H2O, 0.7 mM [U-100% 13C; U-100% 15N] D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMH2O-1[U-100% 15N]0.4-0.81
0.7 mMD2O-2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.05 / pH: 6.3 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
RECOORDscriptsrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2380 / NOE intraresidue total count: 486 / NOE long range total count: 772 / NOE medium range total count: 416 / NOE sequential total count: 706
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.0214 Å / Distance rms dev error: 0.0007 Å

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