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- PDB-5u9b: Solution structure of the zinc fingers 1 and 2 of MBNL1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5u9b
TitleSolution structure of the zinc fingers 1 and 2 of MBNL1 in complex with human cardiac troponin T pre-mRNA
Components
  • Muscleblind-like protein 1
  • RNA (5'-R(P*GP*UP*CP*UP*CP*GP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Zinc fingers RNA-binding / Structure from MOLMOL / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development ...regulatory region RNA binding / myoblast differentiation / embryonic limb morphogenesis / regulation of RNA splicing / RNA splicing / mRNA processing / cytoplasmic stress granule / double-stranded RNA binding / nervous system development / in utero embryonic development / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #210 / RNA-binding, Nab2-type zinc finger / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Muscleblind-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPhukan, P.D. / Park, S. / Martinez-Yamout, M.M. / Zeeb, M. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM36643 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T.
Authors: Park, S. / Phukan, P.D. / Zeeb, M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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_conn.pdbx_dist_value
Revision 1.4May 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: Muscleblind-like protein 1
B: RNA (5'-R(P*GP*UP*CP*UP*CP*GP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3274
Polymers15,1962
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Muscleblind-like protein 1 / Triplet-expansion RNA-binding protein


Mass: 10577.180 Da / Num. of mol.: 1 / Fragment: zinc fingers 1 and 2 (UNP residues 1-92)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBNL1, EXP, KIAA0428, MBNL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR56
#2: RNA chain RNA (5'-R(P*GP*UP*CP*UP*CP*GP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 4618.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic33D 1H-15N NOESY
141isotropic23D 1H-13C NOESY
151isotropic23D HNCA
1111isotropic23D CBCA(CO)NH
1101isotropic23D HN(CA)CB
191isotropic23D (H)CCH-TOCSY
181isotropic23D 13C,15N-filtered NOESY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-98% 13C; U-98% 15N] Zinc fingers 1 and 2 of MBNL1, 0.4 mM unlabeled RNA (5'-R(P*GP*UP*CP*UP*CP*GP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3'), 90% H2O/10% D2O
Label: 15N,13C-MBNL / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMZinc fingers 1 and 2 of MBNL1[U-98% 13C; U-98% 15N]1
0.4 mMRNA (5'-R(P*GP*UP*CP*UP*CP*GP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')unlabeled1
Sample conditionsIonic strength: 100 mM NaCl mM / Label: 1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure calculation
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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