BMRB Entry 19153
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19153
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Title: NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R
Deposition date: 2013-04-09 Original release date: 2014-10-13
Authors: Strickland, Madeleine; Williams, Chris; Richards, Emily; Minnall, Leanne; Crump, Matthew; Frago, Susana; Hughes, Jennifer; Garner, Lee; Hoppe, Hans-Jurgen; Rezgui, Dellel; Zaccheo, Oliver; Prince, Stuart; Hassan, Andrew; Whittaker, Sara
Citation: Frago, Susana; Strickland, Madeleine; Hughes, Jennifer; Williams, Christopher; Garner, Lee; Hoppe, Hans-Jurgen; Rezgui, Dellel; Zaccheo, Oliver; Prince, Stuart; Crump, Matthew; Hassan, Andrew. "Directed evolution of structurally selected IGF2R domain 11 binding loop residues generates an IGF2 super-antagonist" EMBO J. ., .-..
Assembly members:
IGF2R, polymer, 142 residues, 15433.671 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):
IGF2R: MKSNEHDDCQVTNPSTGHLF
DLSSLSGRAGFTAAYAKGWG
VYMSICGENENCPPGVGACF
GQTRISVGKANKRLRYVDQV
LQLVYKDGSPCPSKSGLSYK
SVISFVCRPEAGPTNRPMLI
SLDKQTCTLFFSWHTPLACE
LA
- assigned_chemical_shifts
- heteronucl_NOEs
- heteronucl_T1_relaxation
- heteronucl_T2_relaxation
| Data type | Count |
| 1H chemical shifts | 955 |
| 13C chemical shifts | 597 |
| 15N chemical shifts | 151 |
| heteronuclear NOE values | 266 |
| T1 relaxation values | 284 |
| T2 relaxation values | 284 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | IGF2R | 1 |
Entities:
Entity 1, IGF2R 142 residues - 15433.671 Da.
| 1 | MET | LYS | SER | ASN | GLU | HIS | ASP | ASP | CYS | GLN | ||||
| 2 | VAL | THR | ASN | PRO | SER | THR | GLY | HIS | LEU | PHE | ||||
| 3 | ASP | LEU | SER | SER | LEU | SER | GLY | ARG | ALA | GLY | ||||
| 4 | PHE | THR | ALA | ALA | TYR | ALA | LYS | GLY | TRP | GLY | ||||
| 5 | VAL | TYR | MET | SER | ILE | CYS | GLY | GLU | ASN | GLU | ||||
| 6 | ASN | CYS | PRO | PRO | GLY | VAL | GLY | ALA | CYS | PHE | ||||
| 7 | GLY | GLN | THR | ARG | ILE | SER | VAL | GLY | LYS | ALA | ||||
| 8 | ASN | LYS | ARG | LEU | ARG | TYR | VAL | ASP | GLN | VAL | ||||
| 9 | LEU | GLN | LEU | VAL | TYR | LYS | ASP | GLY | SER | PRO | ||||
| 10 | CYS | PRO | SER | LYS | SER | GLY | LEU | SER | TYR | LYS | ||||
| 11 | SER | VAL | ILE | SER | PHE | VAL | CYS | ARG | PRO | GLU | ||||
| 12 | ALA | GLY | PRO | THR | ASN | ARG | PRO | MET | LEU | ILE | ||||
| 13 | SER | LEU | ASP | LYS | GLN | THR | CYS | THR | LEU | PHE | ||||
| 14 | PHE | SER | TRP | HIS | THR | PRO | LEU | ALA | CYS | GLU | ||||
| 15 | LEU | ALA |
Samples:
sample_1: IGF2R, [U-95% 13C; U-95% 15N], 1 mM; D2O, [U-2H], 7%; H2O 93%; sodium azide 100 uM; EDTA 1 mM; sodium acetate 10 mM
sample_2: IGF2R, [U-95% 15N], 1 mM; D2O, [U-2H], 7%; H2O 93%; sodium azide 100 uM; EDTA 1 mM; sodium acetate 10 mM
sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 273 K
sample_conditions_2: pH: 5.5; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| Heteronuclear NOE ratio | sample_2 | isotropic | sample_conditions_2 |
| Heteronuclear NOE ratio | sample_2 | isotropic | sample_conditions_2 |
| T1 experiments | sample_2 | isotropic | sample_conditions_2 |
| T1 experiments | sample_2 | isotropic | sample_conditions_2 |
| T2 experiments | sample_2 | isotropic | sample_conditions_2 |
| T2 experiments | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
ARIA v2.2, Linge, O, . - processing, refinement, structure solution
CING viCing, Doreleijers - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Relax v1.3.9, Palmer, is, him.' - data analysis, processing
SPARKY v2.6, Goddard - data analysis
VNMRJ v0.4, Varian - collection
CCPN_Analysis v2.1, CCPN - chemical shift assignment, data analysis, peak picking
TALOS vTALOS+, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Varian VNMRS 600 MHz
- Varian VNMRS 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts