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- PDB-2lkz: Solution structure of the second RRM domain of RBM5 -

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Basic information

Entry
Database: PDB / ID: 2lkz
TitleSolution structure of the second RRM domain of RBM5
ComponentsRNA-binding protein 5
KeywordsRNA BINDING PROTEIN / RRM
Function / homology
Function and homology information


regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / RNA processing / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / positive regulation of apoptotic process / negative regulation of cell population proliferation / mRNA binding / apoptotic process ...regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / RNA processing / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / positive regulation of apoptotic process / negative regulation of cell population proliferation / mRNA binding / apoptotic process / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RRM (RNA recognition motif) domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSong, Z. / Wu, P. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of the second RRM domain of RBM5 and its unusual binding characters for different RNA targets
Authors: Song, Z. / Wu, P. / Ji, P. / Zhang, J. / Gong, Q. / Wu, J. / Shi, Y.
History
DepositionOct 23, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: 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 / 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 / _struct_ref_seq_dif.details
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 5


Theoretical massNumber of molelcules
Total (without water)10,5181
Polymers10,5181
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 5 / Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma ...Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma antigen NY-REN-9


Mass: 10518.144 Da / Num. of mol.: 1 / Fragment: RRM 2 domain, UNP residues 231-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM5, H37, LUCA15 / Production host: Escherichia coli (E. coli) / References: UniProt: P52756

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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 CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D H(CCO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D 1H-15N NOESY
1922D 1H-13C HSQC
11023D (H)CCH-COSY
11123D (H)CCH-TOCSY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
140 mM sodium phosphate-1, 50 mM sodium chloride-2, 2 mM EDTA-3, 1 mM sodium azide-4, 90% H2O/10% D2O90% H2O/10% D2O
240 mM sodium phosphate-5, 50 mM sodium chloride-6, 2 mM EDTA-7, 1 mM sodium azide-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
40 mMsodium phosphate-11
50 mMsodium chloride-21
2 mMEDTA-31
1 mMsodium azide-41
40 mMsodium phosphate-52
50 mMsodium chloride-62
2 mMEDTA-72
1 mMsodium azide-82
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ProcheckNMRLaskowski and MacArthurrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1474 / NOE intraresidue total count: 306 / NOE long range total count: 433 / NOE medium range total count: 282 / NOE sequential total count: 453 / Hydrogen bond constraints total count: 58
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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