BMRB Entry 11009

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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/BMR11009
MolProbity Validation Chart

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Title:
SOLUTION STRUCTURE OF THE LSM DOMAIN OF Dm EDC3 (ENHANCER OF DECAPPING 3)
Deposition date:
2007-09-20
Original release date:
2008-06-25
Authors:
Truffault, V.; Coles, M.; Tritschler, F.
Citation:

Citation: Tritschler, F.; Eulalio, A.; Truffault, V.; Hartmann, M.; Helms, S.; Schmidt, S.; Coles, M.; Izaurralde, E.; Weichenrieder, O.. "A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting"  Mol. Cell. Biol. 27, 8600-8611 (2007).
PubMed: 17923697

Assembly members:

Assembly members:
Dm_EDC3, polymer, 103 residues, 11104.973 Da.

Natural source:

Natural source:   Common Name: fruit fly   Taxonomy ID: 7227   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Drosophila melanogaster

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: ESCHERICHIA COLI   Vector: PETM60

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dm_EDC3: GAMGPTDQDWIGCAVSIACD EVLGVFQGLIKQISAEEITI VRAFRNGVPLRKQNAEVVLK CTDIRSIDLIEPAKQDLDGH TAPPPVVNKPTPVKLPHFSN ILG

Data sets:
Data typeCount
13C chemical shifts385
15N chemical shifts91
1H chemical shifts631

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Dm EDC31

Entities:

Entity 1, Dm EDC3 103 residues - 11104.973 Da.

1   GLYALAMETGLYPROTHRASPGLNASPTRP
2   ILEGLYCYSALAVALSERILEALACYSASP
3   GLUVALLEUGLYVALPHEGLNGLYLEUILE
4   LYSGLNILESERALAGLUGLUILETHRILE
5   VALARGALAPHEARGASNGLYVALPROLEU
6   ARGLYSGLNASNALAGLUVALVALLEULYS
7   CYSTHRASPILEARGSERILEASPLEUILE
8   GLUPROALALYSGLNASPLEUASPGLYHIS
9   THRALAPROPROPROVALVALASNLYSPRO
10   THRPROVALLYSLEUPROHISPHESERASN
11   ILELEUGLY

Samples:

sample_1: Dm EDC3, [U-100% 15N], 1.2 mM

sample_2: Dm EDC3, [U-100% 13C; U-100% 15N], 0.8 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D CCH-COSYsample_2isotropicsample_conditions_1
3D CCH-TOCSYsample_2isotropicsample_conditions_1
3D CNH-NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D NNH-NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

xwinnmr v3.6, Bruker Biospin - collection, processing

SPARKY v3.110, Goddard - data analysis

PASTA vV0.1, Leutner et al - chemical shift assignment

X-PLOR NIH v2.9.4a, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Bruker DMX 750 MHz

Related Database Links:

PDB
GB AAF49329 ACU33955 EDV51955 EDW41894 EDW94709
REF NP_648992 XP_001972929 XP_002030908 XP_002085281 XP_002094997
SP Q9VVI2
AlphaFold Q9VVI2

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