BMRB Entry 18720
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18720
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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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 524 |
| 15N chemical shifts | 123 |
| 1H chemical shifts | 18 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Dm DCP1 EVH1 domain | 1 |
| 2 | XRN1 DBM peptide | 2 |
Entities:
Entity 1, Dm DCP1 EVH1 domain 133 residues - 15361.304 Da.
| 1 | GLY | PRO | HIS | MET | ALA | ASP | LEU | MET | ALA | ASP | ||||
| 2 | GLU | SER | ILE | THR | ARG | MET | ASN | LEU | ALA | ALA | ||||
| 3 | ILE | LYS | LYS | ILE | ASP | PRO | TYR | ALA | LYS | GLU | ||||
| 4 | ILE | VAL | ASP | SER | SER | SER | HIS | VAL | ALA | PHE | ||||
| 5 | TYR | THR | PHE | ASN | SER | SER | GLN | ASN | GLU | TRP | ||||
| 6 | GLU | LYS | THR | ASP | VAL | GLU | GLY | ALA | PHE | PHE | ||||
| 7 | ILE | TYR | HIS | ARG | ASN | ALA | GLU | PRO | PHE | HIS | ||||
| 8 | SER | ILE | PHE | ILE | ASN | ASN | ARG | LEU | ASN | THR | ||||
| 9 | THR | SER | PHE | VAL | GLU | PRO | ILE | THR | GLY | SER | ||||
| 10 | LEU | GLU | LEU | GLN | SER | GLN | PRO | PRO | PHE | LEU | ||||
| 11 | LEU | TYR | ARG | ASN | GLU | ARG | SER | ARG | ILE | ARG | ||||
| 12 | GLY | PHE | TRP | PHE | TYR | ASN | SER | GLU | GLU | CYS | ||||
| 13 | ASP | ARG | ILE | SER | GLY | LEU | VAL | ASN | GLY | LEU | ||||
| 14 | LEU | LYS | SER | LYS |
Entity 2, XRN1 DBM peptide 38 residues - 4355.992 Da.
| 1 | GLY | PRO | GLN | ASP | PRO | LEU | LEU | GLN | GLN | GLN | ||||
| 2 | ARG | ALA | PRO | PHE | PRO | GLY | GLN | MET | PRO | ASN | ||||
| 3 | LEU | PRO | LYS | PRO | PRO | LEU | PHE | TRP | GLN | GLN | ||||
| 4 | GLU | ALA | GLN | LYS | GLN | GLU | ALA | LEU |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHB | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESYnoN | sample_1 | isotropic | sample_conditions_1 |
| 2D PLUSH-TACSY | sample_1 | isotropic | sample_conditions_1 |
| 3D NNH NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CNH NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CCH NOESY | sample_1 | isotropic | sample_conditions_1 |
| 4D CCANH | sample_1 | isotropic | sample_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 |