BMRB Entry 17479
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17479
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Title: Structure of the human Shwachman-Bodian-Diamond syndrome (SBDS) protein PubMed: 21536732
Deposition date: 2011-02-21 Original release date: 2011-05-05
Authors: Hilcenko, Christine; Freund, Stefan; Warren, Alan
Citation: Finch, Andrew; Hilcenko, Christine; Basse, Nicolas; Drynan, Lesley; Goyenechea, Beatriz; Menne, Tobias; Gonzalez Fernandez, Africa; Simpson, Paul; Arends, Clive; Donadieu, Mark; Bellanne-Chantelot, Jean; Costanzo, Christine; Boone, Michael; McKenzie, Charles; Freund, Andrew; Warren, Stefan. "Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome." Genes Dev. 25, 917-929 (2011).
Assembly members:
human_SBDS, polymer, 252 residues, 28813.812 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
human_SBDS: GSMSIFTPTNQIRLTNVAVV
RMKRAGKRFEIACYKNKVVG
WRSGVEKDLDEVLQTHSVFV
NVSKGQVAKKEDLISAFGTD
DQTEICKQILTKGEVQVSDK
ERHTQLEQMFRDIATIVADK
CVNPETKRPYTVILIERAMK
DIHYSVKTNKSTKQQALEVI
KQLKEKMKIERAHMRLRFIL
PVNEGKKLKEKLKPLIKVIE
SEDYGQQLEIVCLIDPGCFR
EIDELIKKETKGKGSLEVLN
LKDVEEGDEKFE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 953 |
| 15N chemical shifts | 248 |
| 1H chemical shifts | 1642 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | human_SBDS | 1 |
Entities:
Entity 1, human_SBDS 252 residues - 28813.812 Da.
| 1 | GLY | SER | MET | SER | ILE | PHE | THR | PRO | THR | ASN | ||||
| 2 | GLN | ILE | ARG | LEU | THR | ASN | VAL | ALA | VAL | VAL | ||||
| 3 | ARG | MET | LYS | ARG | ALA | GLY | LYS | ARG | PHE | GLU | ||||
| 4 | ILE | ALA | CYS | TYR | LYS | ASN | LYS | VAL | VAL | GLY | ||||
| 5 | TRP | ARG | SER | GLY | VAL | GLU | LYS | ASP | LEU | ASP | ||||
| 6 | GLU | VAL | LEU | GLN | THR | HIS | SER | VAL | PHE | VAL | ||||
| 7 | ASN | VAL | SER | LYS | GLY | GLN | VAL | ALA | LYS | LYS | ||||
| 8 | GLU | ASP | LEU | ILE | SER | ALA | PHE | GLY | THR | ASP | ||||
| 9 | ASP | GLN | THR | GLU | ILE | CYS | LYS | GLN | ILE | LEU | ||||
| 10 | THR | LYS | GLY | GLU | VAL | GLN | VAL | SER | ASP | LYS | ||||
| 11 | GLU | ARG | HIS | THR | GLN | LEU | GLU | GLN | MET | PHE | ||||
| 12 | ARG | ASP | ILE | ALA | THR | ILE | VAL | ALA | ASP | LYS | ||||
| 13 | CYS | VAL | ASN | PRO | GLU | THR | LYS | ARG | PRO | TYR | ||||
| 14 | THR | VAL | ILE | LEU | ILE | GLU | ARG | ALA | MET | LYS | ||||
| 15 | ASP | ILE | HIS | TYR | SER | VAL | LYS | THR | ASN | LYS | ||||
| 16 | SER | THR | LYS | GLN | GLN | ALA | LEU | GLU | VAL | ILE | ||||
| 17 | LYS | GLN | LEU | LYS | GLU | LYS | MET | LYS | ILE | GLU | ||||
| 18 | ARG | ALA | HIS | MET | ARG | LEU | ARG | PHE | ILE | LEU | ||||
| 19 | PRO | VAL | ASN | GLU | GLY | LYS | LYS | LEU | LYS | GLU | ||||
| 20 | LYS | LEU | LYS | PRO | LEU | ILE | LYS | VAL | ILE | GLU | ||||
| 21 | SER | GLU | ASP | TYR | GLY | GLN | GLN | LEU | GLU | ILE | ||||
| 22 | VAL | CYS | LEU | ILE | ASP | PRO | GLY | CYS | PHE | ARG | ||||
| 23 | GLU | ILE | ASP | GLU | LEU | ILE | LYS | LYS | GLU | THR | ||||
| 24 | LYS | GLY | LYS | GLY | SER | LEU | GLU | VAL | LEU | ASN | ||||
| 25 | LEU | LYS | ASP | VAL | GLU | GLU | GLY | ASP | GLU | LYS | ||||
| 26 | PHE | GLU |
Samples:
sample_1: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.48 mM; H2O 90%; D2O 10%
sample_2: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.5 mM; H2O 90%; D2O 10%
sample_3: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.3 mM; H2O 90%; D2O 10%
sample_4: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.4 mM; H2O 90%; D2O 10%
sample_5: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.35 mM; H2O 90%; D2O 10%
sample_6: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.4 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
sample_conditions_3: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
sample_conditions_4: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
sample_conditions_5: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
sample_conditions_6: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCA | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_2 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_2 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCACO | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCA | sample_5 | isotropic | sample_conditions_5 |
| 3D HNCO | sample_5 | isotropic | sample_conditions_5 |
| 3D HN(CO)CA | sample_5 | isotropic | sample_conditions_5 |
| 3D HBHA(CO)NH | sample_5 | isotropic | sample_conditions_5 |
| 3D HNCACB | sample_5 | isotropic | sample_conditions_5 |
| 3D HNCACO | sample_5 | isotropic | sample_conditions_5 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_3 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_6 | isotropic | sample_conditions_6 |
| 2D 1H-13C HSQC | sample_6 | isotropic | sample_conditions_6 |
| 3D HCCH-TOCSY | sample_6 | isotropic | sample_conditions_6 |
| 3D HCCH-COSY | sample_6 | isotropic | sample_conditions_6 |
| 3D HN(CAN)NH | sample_2 | isotropic | sample_conditions_2 |
| 3D (H)CC(CO)NH | sample_2 | isotropic | sample_conditions_2 |
| 3D H(CCCO)NH | sample_2 | isotropic | sample_conditions_2 |
Software:
SPARKY v3, Goddard - chemical shift assignment, peak picking
TOPSPIN v2.1, Bruker Biospin - processing
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker DRX 900 MHz
Related Database Links:
| BMRB | 16119 |
| PDB | |
| DBJ | BAA91905 BAB23803 BAB29487 BAB31612 BAE40670 |
| EMBL | CAH91068 |
| GB | AAH03849 AAH65700 AAH86335 AAI04586 AAN77490 |
| REF | NP_001008290 NP_001029611 NP_001125618 NP_001231322 NP_057122 |
| SP | P70122 Q3SWZ6 Q5RAZ2 Q5RK30 Q9Y3A5 |
| TPG | DAA15388 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts