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- PDB-2mtv: Solution Structure of the YTH Domain of YT521-B in complex with N... -

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Basic information

Entry
Database: PDB / ID: 2mtv
TitleSolution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA
Components
  • RNA_(5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')
  • YTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN/RNA / YTH / m6A / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear body / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / YTH domain-containing protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsTheler, D. / Dominguez, C. / Blatter, M. / Boudet, J. / Allain, F.H.-T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.
Authors: Theler, D. / Dominguez, C. / Blatter, M. / Boudet, J. / Allain, F.H.
History
DepositionSep 1, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 2.0May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: RNA_(5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)19,3972
Polymers19,3972
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YTH domain-containing protein 1 / Putative splicing factor YT521 / RA301-binding protein


Mass: 17508.191 Da / Num. of mol.: 1 / Fragment: UNP residues 347-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ythdc1, Yt521 / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QY02
#2: RNA chain RNA_(5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')


Mass: 1889.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Sequence detailsAUTHOR STATED THAT T253S IS NOT A MUTATION BUT A CONFLICT IN UNP.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-1H TOCSY
1532D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D H(CCO)NH
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11432D 1H-13C HSQC aliphatic
11532D 1H-13C HSQC aromatic
11613D C(CO)NH
11722D 1H -1H NOESY 13C F1-filtered F2-filtered
11823D 1H-13C NOESY 13C F1-edited F3-filtered
11912D 1H -1H NOESY 13C15N F2-filtered

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] protein_1, 0.8 mM RNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3'), 25 mM sodium phosphate, 25 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 13C; U-99% 15N] protein_1, 0.8 mM RNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3'), 25 mM sodium phosphate, 25 mM sodium chloride, 10 mM beta-mercaptoethanol, 100% D2O100% D2O
30.8 mM [U-99% 15N] protein_1, 0.8 mM RNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3'), 25 mM sodium phosphate, 25 mM sodium chloride, 10 mM beta-mercaptoethanol, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1-1[U-99% 13C; U-99% 15N]1
0.8 mMRNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')-21
25 mMsodium phosphate-31
25 mMsodium chloride-41
10 mMbeta-mercaptoethanol-51
0.8 mMentity_1-6[U-99% 13C; U-99% 15N]2
0.8 mMRNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')-72
25 mMsodium phosphate-82
25 mMsodium chloride-92
10 mMbeta-mercaptoethanol-102
0.8 mMentity_1-11[U-99% 15N]3
0.8 mMRNA (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3')-123
25 mMsodium phosphate-133
25 mMsodium chloride-143
10 mMbeta-mercaptoethanol-153
Sample conditionspH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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