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- PDB-2lk1: Solution structure and binding studies of the RanBP2-type zinc fi... -

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Basic information

Entry
Database: PDB / ID: 2lk1
TitleSolution structure and binding studies of the RanBP2-type zinc finger of RBM5
ComponentsRNA-binding protein 5
KeywordsRNA BINDING PROTEIN / Zinc finger
Function / homology
Function and homology information


spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / 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 ...spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / 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 / metal ion binding / nucleus
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 / 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
Similarity search - Domain/homology
9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid / RNA-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, Energy minimization
Model detailsclosest to the average, model 5
AuthorsFarina, B. / Pellecchia, M.
CitationJournal: Chembiochem / Year: 2011
Title: Targeting Zinc Finger Domains with Small Molecules: Solution Structure and Binding Studies of the RanBP2-Type Zinc Finger of RBM5.
Authors: Farina, B. / Fattorusso, R. / Pellecchia, M.
History
DepositionSep 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0883
Polymers3,7341
Non-polymers3542
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide 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: 3734.449 Da / Num. of mol.: 1 / Fragment: RanBP2-type zinc finger residues 181-210 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P52756
#2: Chemical ChemComp-AQN / 9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid


Mass: 288.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 100 uM RBM5-ZF1, 150 uM ZINC ION, 500 uM AQN, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 uMRBM5-ZF1-11
150 uMZINC ION-21
500 uMAQN-31
Sample conditionsIonic strength: 0 / pH: 5.7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPINv2.1Bruker Biospincollection
TOPSPINv2.1Bruker Biospindata analysis
CARAv1.5,v1.8Keller and Wuthrichchemical shift assignment
CARAv1.5,v1.8Keller and Wuthrichpeak picking
CYANAv2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAv2.1Guntert, Mumenthaler and Wuthrichrefinement
SYBYLTriposenergy minimization
SYBYLTriposrefinement
RefinementMethod: simulated annealing, Energy minimization / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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