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- PDB-2n82: solution structure of the complex of microRNA 20b pre-element wit... -

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Basic information

Entry
Database: PDB / ID: 2n82
Titlesolution structure of the complex of microRNA 20b pre-element with Rbfox RRM
Components
  • RNA (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')
  • RNA binding protein fox-1 homolog 1
KeywordsRNA BINDING PROTEIN/RNA / microRNA / RRM / Rbfox / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing ...regulation of skeletal muscle cell differentiation / RNA transport / nuclear stress granule / MECP2 regulates transcription factors / regulation of alternative mRNA splicing, via spliceosome / neuromuscular process controlling balance / RNA splicing / mRNA 3'-UTR binding / trans-Golgi network / mRNA processing / cytoplasmic stress granule / nervous system development / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
: / RNA binding protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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 protein Fox-1 / Fox-1 C-terminal domain / Calcitonin gene-related peptide regulator C terminal / FOX1, 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 / RNA (> 10) / RNA binding protein fox-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / restrained simulated annealing
AuthorsYang, F. / Chen, Y. / Varani, G.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer.
Authors: Chen, Y. / Zubovic, L. / Yang, F. / Godin, K. / Pavelitz, T. / Castellanos, J. / Macchi, P. / Varani, G.
History
DepositionSep 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 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
Revision 1.3May 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 (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')
B: RNA binding protein fox-1 homolog 1


Theoretical massNumber of molelcules
Total (without water)19,1502
Polymers19,1502
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-6 kcal/mol
Surface area10350 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')


Mass: 7318.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein RNA binding protein fox-1 homolog 1 / Ataxin-2-binding protein 1 / Fox-1 homolog A / Hexaribonucleotide-binding protein 1


Mass: 11831.339 Da / Num. of mol.: 1 / Fragment: UNP residues 109-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFOX1, A2BP, A2BP1, FOX1, HRNBP1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWB1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D F1-, F2-filtered 1H-1H NOESY
2222D F1-, F2-filtered 1H-1H NOESY
2322D 1H-1H TOCSY
2422D 1H-13C HSQC
2523D 1H-13C NOESY
2612D 1H-15N HSQC
2713D 1H-15N NOESY
2813D CBCA(CO)NH
2913D HN(CA)CB
21013D HNCO
21113D HBHA(CO)NH
21223D (H)CCH-TOCSY
21323D CCH-TOCSY
21432D 1H-13C HSQC
21533D 1H-13C NOESY
11642D 1H-15N HSQC
21723D 13C F1-filtered, F3-edited NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 1 mM [U-99% 13C; U-99% 15N] Rbfox RRM, 90% H2O/10% D2O90% H2O/10% D2O
21 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 1 mM [U-99% 13C; U-99% 15N] Rbfox RRM, 100% D2O100% D2O
31 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 1 mM Rbfox RRM, 100% D2O100% D2O
41 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 1 mM Rbfox RRM, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmiR-20b-11
10 mMsodium phosphate-21
20 mMsodium chloride-31
1 mMRbfox RRM-4[U-99% 13C; U-99% 15N]1
1 mMmiR-20b-52
10 mMsodium phosphate-62
20 mMsodium chloride-72
1 mMRbfox RRM-8[U-99% 13C; U-99% 15N]2
1 mMmiR-20b-9[U-99% 13C; U-99% 15N]3
10 mMsodium phosphate-103
20 mMsodium chloride-113
1 mMRbfox RRM-123
1 mMmiR-20b-13[U-99% 13C; U-99% 15N]4
10 mMsodium phosphate-144
20 mMsodium chloride-154
1 mMRbfox RRM-164
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 279 K
26.5 ambient 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
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
CcpNMRCCPNdata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: restrained simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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