BMRB Entry 17166
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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/BMR17166
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Title: Prion-like conversion during amyloid formation at atomic resolution PubMed: 21255727
Deposition date: 2010-09-03 Original release date: 2011-02-04
Authors: Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Homans, Steve; Radford, Sheena
Citation: Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Homans, Steve; Radford, Sheena. "Conformational Conversion during Amyloid Formation at Atomic Resolution" Mol. Cell. 41, 161-172 (2011).
Assembly members:
dN6, polymer, 94 residues, 11138.4564 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):
dN6: MIQVYSRHPAENGKSNFLNC
YVSGFHPSDIEVDLLKNGER
IEKVEHSDLSFSKDWSFYLL
YYTEFTPTEKDEYACRVNHV
TLSQPKIVKWDRDM
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 423 |
| 15N chemical shifts | 97 |
| 1H chemical shifts | 650 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | dN6 | 1 |
Entities:
Entity 1, dN6 94 residues - 11138.4564 Da.
| 1 | MET | ILE | GLN | VAL | TYR | SER | ARG | HIS | PRO | ALA | ||||
| 2 | GLU | ASN | GLY | LYS | SER | ASN | PHE | LEU | ASN | CYS | ||||
| 3 | TYR | VAL | SER | GLY | PHE | HIS | PRO | SER | ASP | ILE | ||||
| 4 | GLU | VAL | ASP | LEU | LEU | LYS | ASN | GLY | GLU | ARG | ||||
| 5 | ILE | GLU | LYS | VAL | GLU | HIS | SER | ASP | LEU | SER | ||||
| 6 | PHE | SER | LYS | ASP | TRP | SER | PHE | TYR | LEU | LEU | ||||
| 7 | TYR | TYR | THR | GLU | PHE | THR | PRO | THR | GLU | LYS | ||||
| 8 | ASP | GLU | TYR | ALA | CYS | ARG | VAL | ASN | HIS | VAL | ||||
| 9 | THR | LEU | SER | GLN | PRO | LYS | ILE | VAL | LYS | TRP | ||||
| 10 | ASP | ARG | ASP | MET |
Samples:
15N13C: dN6, [U-100% 13C; U-100% 15N], 0.5 ± 5e-05 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; H2O 90%; D2O 10%
15N13C_d2o: dN6, [U-100% 13C; U-100% 15N], 1.0 ± 0.0001 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; D2O 100%
Structure: ionic strength: 0.040 M; pH: 7.500; pressure: 1.000 atm; temperature: 298.000 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC/HMQC | 15N13C | isotropic | Structure |
| 3D HNCA | 15N13C | isotropic | Structure |
| 3D HNCACB | 15N13C | isotropic | Structure |
| CBCACONH (H[N[co[{CA|ca[C]}]]]) | 15N13C | isotropic | Structure |
| 3D HN(CO)CA | 15N13C | isotropic | Structure |
| 3D HNCO | 15N13C | isotropic | Structure |
| 3D HCCH-TOCSY | 15N13C | isotropic | Structure |
| 3D HCCH-COSY | 15N13C | isotropic | Structure |
| 2D 1H-13C HSQC/HMQC | 15N13C | isotropic | Structure |
| 2D 1H-13C HSQC/HMQC | 15N13C | isotropic | Structure |
| C_TOCSY (hC_CH.TOCSY) | 15N13C | isotropic | Structure |
| 3D HCCH-TOCSY | 15N13C | isotropic | Structure |
| 3D 1H-13C NOESY | 15N13C_d2o | isotropic | Structure |
| 2D 1H-13C HSQC/HMQC | 15N13C | isotropic | Structure |
| 2D 1H-13C HSQC/HMQC | 15N13C_d2o | isotropic | Structure |
| 3D 1H-13C NOESY | 15N13C_d2o | isotropic | Structure |
| 3D 1H-15N NOESY | 15N13C | isotropic | Structure |
| 15NNOESY_CORR | 15N13C_d2o | solution | Structure |
| HNCA | 15N13C_d2o | solution | Structure |
Software:
ARIA v2.1, Linge, O'Donoghue and Nilges - refinement
AutoDep v4.3, PDBe - collection
ANALYSIS v2.1, CCPN - data analysis
NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v5.22, Johnson, One Moon Scientific - data analysis
PASD_algorithm v1.0, Kuszewski et al. - de novo structure calculation
VNMR v6.1c, VARIAN - collection
VNMR_6.1C vany, Varian - collection
X-PLOR NIH v2.17, Schwieters, Kusyewski, Tjandra and Clore - structure solution
NMR spectrometers:
- Varian INOVA 749 MHz
- Varian INOVA 500 MHz
- Varian INOVA 600 MHz
- Varian IVANOVA 749 MHz
Related Database Links:
| UNP | B2MG_HUMAN |
| BMRB | 15480 16587 17165 19099 19113 19116 19118 19119 19120 19121 19122 19123 3078 3079 |
| PDB | |
| DBJ | BAA35182 BAG38125 BAG64583 BAG72952 |
| EMBL | CAA23830 CAG33347 CAH92078 |
| GB | AAA51811 AAA87972 AAA88008 AAB25312 AAB35347 |
| REF | NP_001009066 NP_001127503 NP_004039 XP_004056148 XP_004056149 |
| SP | P16213 P61769 P61770 P61771 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts