BMRB Entry 34219
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34219
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Solution structure of the MRH domain of Yos9 complexed with alpha3,alpha6-Man5 PubMed: 30066206
Deposition date: 2017-12-14 Original release date: 2019-01-28
Authors: Kniss, A.; Kazemi, S.; Lohr, F.; Guntert, P.; Dotsch, V.
Citation: Kniss, Andreas; Kazemi, Sina; Lohr, Frank; Berger, Maren; Rogov, Vladimir; Guntert, Peter; Sommer, Thomas; Jarosch, Ernst; Dotsch, Volker. "Structural investigation of glycan recognition by the ERAD quality control lectin Yos9" J. Biomol. NMR 72, 1-10 (2018).
Assembly members:
entity_1, polymer, 162 residues, 18328.627 Da.
Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GASNSEKTALLTKTLNQGVK
TIFDKLNERCIFYQAGFWIY
EYCPGIEFVQFHGRVNTKTG
EIVNRDESLVYRLGKPKANV
EEREFELLYDDVGYYISEII
GSGDICDVTGAERMVEIQYV
CGGSNSGPSTIQWVRETKIC
VYEAQVTIPELCNLELLAKN
ED
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 676 |
| 15N chemical shifts | 148 |
| 1H chemical shifts | 1067 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 162 residues - 18328.627 Da.
| 1 | GLY | ALA | SER | ASN | SER | GLU | LYS | THR | ALA | LEU | ||||
| 2 | LEU | THR | LYS | THR | LEU | ASN | GLN | GLY | VAL | LYS | ||||
| 3 | THR | ILE | PHE | ASP | LYS | LEU | ASN | GLU | ARG | CYS | ||||
| 4 | ILE | PHE | TYR | GLN | ALA | GLY | PHE | TRP | ILE | TYR | ||||
| 5 | GLU | TYR | CYS | PRO | GLY | ILE | GLU | PHE | VAL | GLN | ||||
| 6 | PHE | HIS | GLY | ARG | VAL | ASN | THR | LYS | THR | GLY | ||||
| 7 | GLU | ILE | VAL | ASN | ARG | ASP | GLU | SER | LEU | VAL | ||||
| 8 | TYR | ARG | LEU | GLY | LYS | PRO | LYS | ALA | ASN | VAL | ||||
| 9 | GLU | GLU | ARG | GLU | PHE | GLU | LEU | LEU | TYR | ASP | ||||
| 10 | ASP | VAL | GLY | TYR | TYR | ILE | SER | GLU | ILE | ILE | ||||
| 11 | GLY | SER | GLY | ASP | ILE | CYS | ASP | VAL | THR | GLY | ||||
| 12 | ALA | GLU | ARG | MET | VAL | GLU | ILE | GLN | TYR | VAL | ||||
| 13 | CYS | GLY | GLY | SER | ASN | SER | GLY | PRO | SER | THR | ||||
| 14 | ILE | GLN | TRP | VAL | ARG | GLU | THR | LYS | ILE | CYS | ||||
| 15 | VAL | TYR | GLU | ALA | GLN | VAL | THR | ILE | PRO | GLU | ||||
| 16 | LEU | CYS | ASN | LEU | GLU | LEU | LEU | ALA | LYS | ASN | ||||
| 17 | GLU | ASP |
Samples:
sample_1: MRH domain of Yos9, [U-98% 13C; U-98% 15N], 0.55 mM; alpha3,alpha6-Man5 8.25 mM
sample_2: MRH domain of Yos9, [U-98% 13C; U-98% 15N], 1 mM; alpha3,alpha6-Man5 15 mM
sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C 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 HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D(HB)CB(CGCD)HD | sample_1 | isotropic | sample_conditions_1 |
| 2D (H)CB(CGCC)H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
SPARKY v3.13, Goddard - chemical shift assignment
CYANA v3.9, Guntert, P. - structure calculation
OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz
- Bruker Avance 950 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts