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- PDB-7fbr: Solution structure of The first RNA binding domain of Matrin-3 -

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Basic information

Entry
Database: PDB / ID: 7fbr
TitleSolution structure of The first RNA binding domain of Matrin-3
ComponentsMatrin-3
KeywordsRNA BINDING PROTEIN / RRM / ALS/FTD / nuclear matrix protein / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


heart valve development / blastocyst formation / miRNA binding / ventricular septum development / post-transcriptional regulation of gene expression / activation of innate immune response / nuclear matrix / innate immune response / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Matrin-3, RNA recognition motif 1 / Matrin-3, RNA recognition motif 2 / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMuto, Y. / Kobayashi, N. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biomol.Nmr Assign. / Year: 2022
Title: 1 H, 13 C and 15 N resonance assignments and solution structures of the two RRM domains of Matrin-3.
Authors: He, F. / Kuwasako, K. / Takizawa, M. / Takahashi, M. / Tsuda, K. / Nagata, T. / Watanabe, S. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y.
History
DepositionJul 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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

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Assembly

Deposited unit
A: Matrin-3


Theoretical massNumber of molelcules
Total (without water)11,3521
Polymers11,3521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrin-3


Mass: 11351.972 Da / Num. of mol.: 1 / Mutation: S397R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Matr3
Production host: Cell-free gateway cloning vector N-term 8xHis eGFP pCellFree_G03 (others)
References: UniProt: Q8K310

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D 13C,15N-SEPARATED NOESY SPECTRA

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] RNA binding protein, 90% H2O/10% D2O
Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: RNA binding protein / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 20mM D-Tris-HCL (PH7.0); 100mM NaCl; 1mM D-DTT;0.02% NaN3
Ionic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
KUJIRA0.863N. Kobayashi, T. Kigawa, S. Yokoyamachemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificpeak picking
TopSpin2.1Bruker Biospincollection
TALOS2007Cornilescu, Delaglio and Baxgeometry optimization
NMRPipe2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 2063 NOE-derived distance constrains, 41 main chain dihedral angle constraints based on TALOS program and 7 side chain dihedral constraints based on NOE pattern.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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