BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 18720

Title: The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide   PubMed: 23142987

Deposition date: 2012-09-17 Original release date: 2012-10-15

Authors: Truffault, Vincent

Citation: Braun, Joerg; Truffault, Vincent; Boland, Andreas; Huntzinger, Eric; Chang, Chung-Te; Haas, Gabrielle; Weichenrieder, Oliver; Coles, Murray; Izaurralde, Elisa. "A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation."  Nat. Struct. Mol. Biol. 19, 1324-1331 (2012).

Assembly members:
Dm_DCP1_EVH1_domain, polymer, 133 residues, 15361.304 Da.
XRN1_DBM, polymer, 38 residues, 4355.992 Da.

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

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

Entity Sequences (FASTA):
Dm_DCP1_EVH1_domain: GPHMADLMADESITRMNLAA IKKIDPYAKEIVDSSSHVAF YTFNSSQNEWEKTDVEGAFF IYHRNAEPFHSIFINNRLNT TSFVEPITGSLELQSQPPFL LYRNERSRIRGFWFYNSEEC DRISGLVNGLLKSK
XRN1_DBM: GPQDPLLQQQRAPFPGQMPN LPKPPLFWQQEAQKQEAL

Data sets:
Data typeCount
13C chemical shifts524
15N chemical shifts123
1H chemical shifts18

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Dm DCP1 EVH1 domain1
2XRN1 DBM peptide2

Entities:

Entity 1, Dm DCP1 EVH1 domain 133 residues - 15361.304 Da.

1   GLYPROHISMETALAASPLEUMETALAASP
2   GLUSERILETHRARGMETASNLEUALAALA
3   ILELYSLYSILEASPPROTYRALALYSGLU
4   ILEVALASPSERSERSERHISVALALAPHE
5   TYRTHRPHEASNSERSERGLNASNGLUTRP
6   GLULYSTHRASPVALGLUGLYALAPHEPHE
7   ILETYRHISARGASNALAGLUPROPHEHIS
8   SERILEPHEILEASNASNARGLEUASNTHR
9   THRSERPHEVALGLUPROILETHRGLYSER
10   LEUGLULEUGLNSERGLNPROPROPHELEU
11   LEUTYRARGASNGLUARGSERARGILEARG
12   GLYPHETRPPHETYRASNSERGLUGLUCYS
13   ASPARGILESERGLYLEUVALASNGLYLEU
14   LEULYSSERLYS

Entity 2, XRN1 DBM peptide 38 residues - 4355.992 Da.

1   GLYPROGLNASPPROLEULEUGLNGLNGLN
2   ARGALAPROPHEPROGLYGLNMETPROASN
3   LEUPROLYSPROPROLEUPHETRPGLNGLN
4   GLUALAGLNLYSGLNGLUALALEU

Samples:

sample_1: Dm_DCP1_EVH1_domain, [U-100% 15N], 0.4 mM; Dm_DCP1_EVH1_domain, [U-100% 13C; U-100% 15N], 0.7 mM; XRN1_DBM, [U-100% 15N], 0.4 mM; XRN1_DBM, [U-100% 13C; U-100% 15N], 0.7 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
2D NOESYnoNsample_1isotropicsample_conditions_1
2D PLUSH-TACSYsample_1isotropicsample_conditions_1
3D NNH NOESYsample_1isotropicsample_conditions_1
3D CNH NOESYsample_1isotropicsample_conditions_1
3D CCH NOESYsample_1isotropicsample_conditions_1
4D CCANHsample_1isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
GB AAF47089 AAX94785 ACL88332 ACZ94554 EDV56888 AAF48958 AAK93099 ACZ95330
REF NP_001163282 NP_611842 XP_001976488 XP_002040166 XP_002045212 NP_001162796 NP_523408
EMBL CAB43711