BMRB Entry 30584
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30584
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Title: Solution structure of human myeloid-derived growth factor PubMed: 31819058
Deposition date: 2019-03-07 Original release date: 2019-11-05
Authors: Bortnov, V.; Tonelli, M.; Lee, W.; Markley, J.; Mosher, D.
Citation: Bortnov, Valeriu; Tonelli, Marco; Lee, Woonghee; Lin, Ziqing; Annis, Douglas; Demerdash, Omar; Bateman, Alex; Mitchell, Julie; Ge, Ying; Markley, John; Mosher, Deane. "Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum" Nat. Comm. 10, 5612-5612 (2019).
Assembly members:
entity_1, polymer, 147 residues, 16286.207 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):
entity_1: GSKGTVSEPTTVAFDVRPGG
VVHSFSHNVGPGDKYTCMFT
YASQGGTNEQWQMSLGTSED
HQHFTCTIWRPQGKSYLYFT
QFKAEVRGAEIEYAMAYSKA
AFERESDVPLKTEEFEVTKT
AVAHRPGAFKAELSKLVIVA
KASRTEL
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 630 |
| 15N chemical shifts | 149 |
| 1H chemical shifts | 972 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 147 residues - 16286.207 Da.
| 1 | GLY | SER | LYS | GLY | THR | VAL | SER | GLU | PRO | THR | ||||
| 2 | THR | VAL | ALA | PHE | ASP | VAL | ARG | PRO | GLY | GLY | ||||
| 3 | VAL | VAL | HIS | SER | PHE | SER | HIS | ASN | VAL | GLY | ||||
| 4 | PRO | GLY | ASP | LYS | TYR | THR | CYS | MET | PHE | THR | ||||
| 5 | TYR | ALA | SER | GLN | GLY | GLY | THR | ASN | GLU | GLN | ||||
| 6 | TRP | GLN | MET | SER | LEU | GLY | THR | SER | GLU | ASP | ||||
| 7 | HIS | GLN | HIS | PHE | THR | CYS | THR | ILE | TRP | ARG | ||||
| 8 | PRO | GLN | GLY | LYS | SER | TYR | LEU | TYR | PHE | THR | ||||
| 9 | GLN | PHE | LYS | ALA | GLU | VAL | ARG | GLY | ALA | GLU | ||||
| 10 | ILE | GLU | TYR | ALA | MET | ALA | TYR | SER | LYS | ALA | ||||
| 11 | ALA | PHE | GLU | ARG | GLU | SER | ASP | VAL | PRO | LEU | ||||
| 12 | LYS | THR | GLU | GLU | PHE | GLU | VAL | THR | LYS | THR | ||||
| 13 | ALA | VAL | ALA | HIS | ARG | PRO | GLY | ALA | PHE | LYS | ||||
| 14 | ALA | GLU | LEU | SER | LYS | LEU | VAL | ILE | VAL | ALA | ||||
| 15 | LYS | ALA | SER | ARG | THR | GLU | LEU |
Samples:
sample_1: MYDGF, [U-15N; U-13C], 8.25 mg/mL; sodium phosphate 9 mM; sodium chloride 135 mM; DSS 15 uM; sodium azide 0.02 % w/v
sample_conditions_1: ionic strength: 135 mM; pH: 6; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H,15N-HSQC NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H,13C-HSQC NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H,13C-HSQC NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCD)HD aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCDCE)HDHE aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H,15N-HSQC NOESY 1H,13C-HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
VNMR v4.2, Varian - collection
TopSpin v3.5, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRFAM-SPARKY, W. Lee, M. Tonelli and J.L. Markley - chemical shift assignment, peak picking
I-PINE, W. Lee, A. Bahrami, H. Dashti, H.R. Eghbalnia, M. Tonelli, W.M. Westler, J.L. Markley - chemical shift assignment
PONDEROSA-C/S, W. Lee, J.L. Stark, J.L. Markley - refinement, structure calculation
TALOS-N, Shen and Bax - structure calculation
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
PyMOL, Schroedinger, Inc. - refinement
NMR spectrometers:
- Varian VNS 800 MHz
- Bruker AvanceIII 600 MHz
- Bruker AvanceIII 900 MHz
- Varian VNS 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts