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Biological Magnetic Resonance Data Bank


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BMRB Entry 25188

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25188
MolProbity Validation Chart

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Title: Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA   PubMed: 25389274

Deposition date: 2014-09-01 Original release date: 2014-11-17

Authors: Theler, Dominik; Dominguez, Cyril; Blatter, Markus; Boudet, Julien; Allain, Frederic

Citation: Theler, Dominik; Dominguez, Cyril; Blatter, Markus; Boudet, Julien; Allain, Frederic. "Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA"  Nucleic Acids Res. 42, 13911-13919 (2014).

Assembly members:
entity_1, polymer, 156 residues, 17508.334 Da.
RNA_(5'-R(*UP*GP*(6MA)P*CP*AP*C)-3'), polymer, 6 residues, 1873.230 Da.

Natural source:   Common Name: Norway rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: QTSKLKSVLQDARFFLIKSN NHENVSLAKAKGVWSTLPVN EKKLNLAFRSARSVILIFSV RESGKFQGFARLSSESHHGG SPIHWVLPAGMSAKMLGGVF KIDWICRRELPFTKSAHLTN PWNEHKPVKIGRDGQEIELE CGTQLCLLFPPDESID
RNA_(5'-R(*UP*GP*(6MA)P*CP*AP*C)-3'): UGXCAC

Data sets:
Data typeCount
13C chemical shifts683
15N chemical shifts155
1H chemical shifts1138

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3')2

Entities:

Entity 1, entity_1 156 residues - 17508.334 Da.

1   GLNTHRSERLYSLEULYSSERVALLEUGLN
2   ASPALAARGPHEPHELEUILELYSSERASN
3   ASNHISGLUASNVALSERLEUALALYSALA
4   LYSGLYVALTRPSERTHRLEUPROVALASN
5   GLULYSLYSLEUASNLEUALAPHEARGSER
6   ALAARGSERVALILELEUILEPHESERVAL
7   ARGGLUSERGLYLYSPHEGLNGLYPHEALA
8   ARGLEUSERSERGLUSERHISHISGLYGLY
9   SERPROILEHISTRPVALLEUPROALAGLY
10   METSERALALYSMETLEUGLYGLYVALPHE
11   LYSILEASPTRPILECYSARGARGGLULEU
12   PROPHETHRLYSSERALAHISLEUTHRASN
13   PROTRPASNGLUHISLYSPROVALLYSILE
14   GLYARGASPGLYGLNGLUILEGLULEUGLU
15   CYSGLYTHRGLNLEUCYSLEULEUPHEPRO
16   PROASPGLUSERILEASP

Entity 2, RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3') 6 residues - 1873.230 Da.

1   UG6MZCAC

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.8 mM; RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3') 0.8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; beta-mercaptoethanol 10 mM; D2O 10%; H2O 90%

sample_2: entity_1, [U-99% 13C; U-99% 15N], 0.8 mM; RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3') 0.8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; beta-mercaptoethanol 10 mM; D2O 100%

sample_3: entity_1, [U-99% 15N], 0.8 mM; RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3') 0.8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; beta-mercaptoethanol 10 mM; D2O 100%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
2D 1H -1H NOESY 13C F1-filtered F2-filteredsample_2isotropicsample_conditions_1
3D 1H-13C NOESY 13C F1-edited F3-filteredsample_2isotropicsample_conditions_1
2D 1H -1H NOESY 13C15N F2-filteredsample_1isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

TOPSPIN, Bruker Biospin - collection, processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

PDB
DBJ BAA23885 BAB71181 BAB85552 BAD32590 BAG10510
EMBL CAH91339
GB AAD55973 AAH22697 AAH41119 AAH53863 AAI02815
REF NP_001026902 NP_001039985 NP_001125792 NP_588611 NP_596914
SP E9Q5K9 Q96MU7 Q9QY02
TPG DAA28607

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts