BMRB Entry 17703

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17703
MolProbity Validation Chart

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Title:
Backbone and stereo-specific Ile(d1), Leu, Val methyl sidechain chemical shift assignments of RDE-4 (1-243)
Deposition date:
2011-06-14
Original release date:
2011-10-26
Authors:
Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar
Citation:

Citation: Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar. "Backbone and sidechain methyl Ile (1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans."  Biomol. NMR Assignments 6, 143-146 (2012).
PubMed: 22002349

Assembly members:

Assembly members:
RDE-4DC, polymer, 251 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: nematode   Taxonomy ID: 6239   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RDE-4DC: MDLTKLTFESVFGGSDVPMK PSRSEDNKTPRNRTDLEMFL KKTPLMVLEEAAKAVYQKTP TWGTVELPEGFEMTLILNEI TVKGQATSKKAARQKAAVEY LRKVVEKGKHEIFFIPGTTK EEALSNIDQISDKAEELKRS TSDAVQDNDNDDSIPTSAEF PPGISPTENWVGKLQEKSQK SKLQAPIYEDSKNERTERFL VICTMCNQKTRGIRSKKKDA KNLAAWLMWKALEDGIESLE SYDLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts775
15N chemical shifts226
1H chemical shifts434

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RDE-4DC1

Entities:

Entity 1, RDE-4DC 251 residues - Formula weight is not available

1   METASPLEUTHRLYSLEUTHRPHEGLUSER
2   VALPHEGLYGLYSERASPVALPROMETLYS
3   PROSERARGSERGLUASPASNLYSTHRPRO
4   ARGASNARGTHRASPLEUGLUMETPHELEU
5   LYSLYSTHRPROLEUMETVALLEUGLUGLU
6   ALAALALYSALAVALTYRGLNLYSTHRPRO
7   THRTRPGLYTHRVALGLULEUPROGLUGLY
8   PHEGLUMETTHRLEUILELEUASNGLUILE
9   THRVALLYSGLYGLNALATHRSERLYSLYS
10   ALAALAARGGLNLYSALAALAVALGLUTYR
11   LEUARGLYSVALVALGLULYSGLYLYSHIS
12   GLUILEPHEPHEILEPROGLYTHRTHRLYS
13   GLUGLUALALEUSERASNILEASPGLNILE
14   SERASPLYSALAGLUGLULEULYSARGSER
15   THRSERASPALAVALGLNASPASNASPASN
16   ASPASPSERILEPROTHRSERALAGLUPHE
17   PROPROGLYILESERPROTHRGLUASNTRP
18   VALGLYLYSLEUGLNGLULYSSERGLNLYS
19   SERLYSLEUGLNALAPROILETYRGLUASP
20   SERLYSASNGLUARGTHRGLUARGPHELEU
21   VALILECYSTHRMETCYSASNGLNLYSTHR
22   ARGGLYILEARGSERLYSLYSLYSASPALA
23   LYSASNLEUALAALATRPLEUMETTRPLYS
24   ALALEUGLUASPGLYILEGLUSERLEUGLU
25   SERTYRASPLEUGLUHISHISHISHISHIS
26   HIS

Samples:

U-15N: RDE-4DC, [U-100% 15N], 200 uM; RDE-4DC, [U-15N]-Lys, 200 uM; RDE-4DC, [U-15N]-(-R)Arg, 200 uM; H20 90%; D20 10%; Potassium phosphate buffer 50 mM; Na2SO4 100 mM

13C_15N_2H: RDE-4DC, [U-100% 13C; U-100% 15N; U-80% 2H], 500 uM; H20 90%; D20 10%; Potassium phosphate buffer 50 mM; Na2SO4 100 mM

U-13C_ILV: RDE-4DC, [U-13C Ile, Leu, Val (rest 12C); U-15N; U-2H], 500 uM; H20 90%; D20 10%; Potassium phosphate buffer 50 mM; Na2SO4 100 mM

U-13C_Me_only_ILV: RDE-4DC, [U-13C,1H Me only Ile, Leu, Val (rest 12C,2H); 15N,1H, Phe; U-15N; U-2H], 500 uM; RDE-4DC, [U-13C,1H Me only Ile, Leu, Val (rest 12C,2H); 15N,1H, Tyr; U-15N; U-2H], 500 uM; H20 90%; D20 10%; Potassium phosphate buffer 50 mM; Na2SO4 100 mM

10%13C: RDE-4DC, [U-10% 13C], 200 uM; H20 90%; D20 10%; Potassium phosphate buffer 50 mM; Na2SO4 100 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCU-15Nisotropicsample_conditions_1
3D HNCO13C_15N_2Hisotropicsample_conditions_1
3D HNCA13C_15N_2Hisotropicsample_conditions_1
3D HN(CA)CB13C_15N_2Hisotropicsample_conditions_1
3D HN(CO)CA13C_15N_2Hisotropicsample_conditions_1
3D HN(COCA)CB13C_15N_2Hisotropicsample_conditions_1
3D HN(CA)CO13C_15N_2Hisotropicsample_conditions_1
3D H(CCO)NHU-13C_ILVisotropicsample_conditions_1
3D (H)C(CO)NHU-13C_ILVisotropicsample_conditions_1
2D 1H-13C HSQC10%13Cisotropicsample_conditions_1
3D 1H-13C NOESY-HSQCU-13C_Me_only_ILVisotropicsample_conditions_1
3D 1H-15N HMQC-NOESY-HSQC13C_15N_2Hisotropicsample_conditions_1
2D 1H-13C HSQCU-13C_Me_only_ILVisotropicsample_conditions_1
3D 1H-15N NOESY-HSQCU-15Nisotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

EMBL CAA83012
GB AAL61544
REF NP_499265

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks