BMRB Entry 30735
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30735
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Title: NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc PubMed: 32227412
Deposition date: 2020-03-10 Original release date: 2020-04-27
Authors: Lee, K.; Fang, Z.; Enomoto, M.; Gasmi-Seabrook, G.; Zheng, L.; Marshall, C.; Ikura, M.
Citation: Lee, K.; Fang, Z.; Enomoto, M.; Seabrook, G.; Zheng, L.; Koide, S.; Ikura, M.; Marshall, C.. "Two Distinct Structures of Membrane-associated Homodimers of GTP- and GDP-bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement." Angew. Chem. Int. Ed. Engl. ., .-. (2020).
Assembly members:
entity_1, polymer, 200 residues, 23234.295 Da.
entity_2, polymer, 184 residues, 21042.959 Da.
entity_PCW, non-polymer, 787.121 Da.
entity_17F, non-polymer, 788.043 Da.
entity_GDP, non-polymer, 443.201 Da.
entity_MG, non-polymer, 24.305 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 K-12
Entity Sequences (FASTA):
entity_1: GPLKLLDNWDSVTSTFSKLR
EQLGPVTQEFWDNLEKETEG
LRQEMSKDLEEVKAKVQPYL
DDFQKKWQEEMELYRQKVEP
LRAELQEGARQKLHELQEKL
SPLGEEMRDRARAHVDALRT
HLAPYSDELRQRLAARLEAL
KENGGARLAEYHAKATEHLS
TLSEKAKPALEDLRQGLLPV
LESFKVSFLSALEEYTKKLN
entity_2: TEYKLVVVGADGVGKSALTI
QLIQNHFVDEYDPTIEDSYR
KQVVIDGETCLLDILDTAGQ
EEYSAMRDQYMRTGEGFLCV
FAINNTKSFEDIHHYREQIK
RVKDSEDVPMVLVGNKCDLP
SRTVDTKQAQDLARSYGIPF
IETSAKTRQGVDDAFYTLVR
EIRKHKEKMSKDGKKKKKKS
KTKC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 40 |
| 15N chemical shifts | 15 |
| 1H chemical shifts | 135 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
| 3 | entity_2, 1 | 2 |
| 4 | entity_2, 2 | 2 |
| 5 | entity_3, 1 | 3 |
| 6 | entity_3, 2 | 3 |
| 7 | entity_3, 3 | 3 |
| 8 | entity_3, 4 | 3 |
| 9 | entity_3, 5 | 3 |
| 10 | entity_3, 6 | 3 |
| 11 | entity_3, 7 | 3 |
| 12 | entity_3, 8 | 3 |
| 13 | entity_3, 9 | 3 |
| 14 | entity_3, 10 | 3 |
| 15 | entity_3, 11 | 3 |
| 16 | entity_3, 12 | 3 |
| 17 | entity_3, 13 | 3 |
| 18 | entity_3, 14 | 3 |
| 19 | entity_3, 15 | 3 |
| 20 | entity_3, 16 | 3 |
| 21 | entity_3, 17 | 3 |
| 22 | entity_3, 18 | 3 |
| 23 | entity_3, 19 | 3 |
| 24 | entity_3, 20 | 3 |
| 25 | entity_3, 21 | 3 |
| 26 | entity_3, 22 | 3 |
| 27 | entity_3, 23 | 3 |
| 28 | entity_3, 24 | 3 |
| 29 | entity_3, 25 | 3 |
| 30 | entity_3, 26 | 3 |
| 31 | entity_3, 27 | 3 |
| 32 | entity_3, 28 | 3 |
| 33 | entity_3, 29 | 3 |
| 34 | entity_3, 30 | 3 |
| 35 | entity_3, 31 | 3 |
| 36 | entity_3, 32 | 3 |
| 37 | entity_3, 33 | 3 |
| 38 | entity_3, 34 | 3 |
| 39 | entity_3, 35 | 3 |
| 40 | entity_3, 36 | 3 |
| 41 | entity_3, 37 | 3 |
| 42 | entity_3, 38 | 3 |
| 43 | entity_3, 39 | 3 |
| 44 | entity_3, 40 | 3 |
| 45 | entity_3, 41 | 3 |
| 46 | entity_3, 42 | 3 |
| 47 | entity_3, 43 | 3 |
| 48 | entity_3, 44 | 3 |
| 49 | entity_3, 45 | 3 |
| 50 | entity_3, 46 | 3 |
| 51 | entity_3, 47 | 3 |
| 52 | entity_3, 48 | 3 |
| 53 | entity_3, 49 | 3 |
| 54 | entity_3, 50 | 3 |
| 55 | entity_3, 51 | 3 |
| 56 | entity_3, 52 | 3 |
| 57 | entity_3, 53 | 3 |
| 58 | entity_3, 54 | 3 |
| 59 | entity_3, 55 | 3 |
| 60 | entity_3, 56 | 3 |
| 61 | entity_3, 57 | 3 |
| 62 | entity_3, 58 | 3 |
| 63 | entity_3, 59 | 3 |
| 64 | entity_3, 60 | 3 |
| 65 | entity_3, 61 | 3 |
| 66 | entity_3, 62 | 3 |
| 67 | entity_3, 63 | 3 |
| 68 | entity_3, 64 | 3 |
| 69 | entity_4, 1 | 4 |
| 70 | entity_4, 2 | 4 |
| 71 | entity_4, 3 | 4 |
| 72 | entity_4, 4 | 4 |
| 73 | entity_4, 5 | 4 |
| 74 | entity_4, 6 | 4 |
| 75 | entity_4, 7 | 4 |
| 76 | entity_4, 8 | 4 |
| 77 | entity_4, 9 | 4 |
| 78 | entity_4, 10 | 4 |
| 79 | entity_4, 11 | 4 |
| 80 | entity_4, 12 | 4 |
| 81 | entity_4, 13 | 4 |
| 82 | entity_4, 14 | 4 |
| 83 | entity_4, 15 | 4 |
| 84 | entity_4, 16 | 4 |
| 85 | entity_5, 1 | 5 |
| 86 | entity_5, 2 | 5 |
| 87 | entity_6, 1 | 6 |
| 88 | entity_6, 2 | 6 |
Entities:
Entity 1, entity_1, 1 200 residues - 23234.295 Da.
| 1 | GLY | PRO | LEU | LYS | LEU | LEU | ASP | ASN | TRP | ASP | |
| 2 | SER | VAL | THR | SER | THR | PHE | SER | LYS | LEU | ARG | |
| 3 | GLU | GLN | LEU | GLY | PRO | VAL | THR | GLN | GLU | PHE | |
| 4 | TRP | ASP | ASN | LEU | GLU | LYS | GLU | THR | GLU | GLY | |
| 5 | LEU | ARG | GLN | GLU | MET | SER | LYS | ASP | LEU | GLU | |
| 6 | GLU | VAL | LYS | ALA | LYS | VAL | GLN | PRO | TYR | LEU | |
| 7 | ASP | ASP | PHE | GLN | LYS | LYS | TRP | GLN | GLU | GLU | |
| 8 | MET | GLU | LEU | TYR | ARG | GLN | LYS | VAL | GLU | PRO | |
| 9 | LEU | ARG | ALA | GLU | LEU | GLN | GLU | GLY | ALA | ARG | |
| 10 | GLN | LYS | LEU | HIS | GLU | LEU | GLN | GLU | LYS | LEU | |
| 11 | SER | PRO | LEU | GLY | GLU | GLU | MET | ARG | ASP | ARG | |
| 12 | ALA | ARG | ALA | HIS | VAL | ASP | ALA | LEU | ARG | THR | |
| 13 | HIS | LEU | ALA | PRO | TYR | SER | ASP | GLU | LEU | ARG | |
| 14 | GLN | ARG | LEU | ALA | ALA | ARG | LEU | GLU | ALA | LEU | |
| 15 | LYS | GLU | ASN | GLY | GLY | ALA | ARG | LEU | ALA | GLU | |
| 16 | TYR | HIS | ALA | LYS | ALA | THR | GLU | HIS | LEU | SER | |
| 17 | THR | LEU | SER | GLU | LYS | ALA | LYS | PRO | ALA | LEU | |
| 18 | GLU | ASP | LEU | ARG | GLN | GLY | LEU | LEU | PRO | VAL | |
| 19 | LEU | GLU | SER | PHE | LYS | VAL | SER | PHE | LEU | SER | |
| 20 | ALA | LEU | GLU | GLU | TYR | THR | LYS | LYS | LEU | ASN |
Entity 2, entity_2, 1 184 residues - 21042.959 Da.
| 1 | THR | GLU | TYR | LYS | LEU | VAL | VAL | VAL | GLY | ALA | ||||
| 2 | ASP | GLY | VAL | GLY | LYS | SER | ALA | LEU | THR | ILE | ||||
| 3 | GLN | LEU | ILE | GLN | ASN | HIS | PHE | VAL | ASP | GLU | ||||
| 4 | TYR | ASP | PRO | THR | ILE | GLU | ASP | SER | TYR | ARG | ||||
| 5 | LYS | GLN | VAL | VAL | ILE | ASP | GLY | GLU | THR | CYS | ||||
| 6 | LEU | LEU | ASP | ILE | LEU | ASP | THR | ALA | GLY | GLN | ||||
| 7 | GLU | GLU | TYR | SER | ALA | MET | ARG | ASP | GLN | TYR | ||||
| 8 | MET | ARG | THR | GLY | GLU | GLY | PHE | LEU | CYS | VAL | ||||
| 9 | PHE | ALA | ILE | ASN | ASN | THR | LYS | SER | PHE | GLU | ||||
| 10 | ASP | ILE | HIS | HIS | TYR | ARG | GLU | GLN | ILE | LYS | ||||
| 11 | ARG | VAL | LYS | ASP | SER | GLU | ASP | VAL | PRO | MET | ||||
| 12 | VAL | LEU | VAL | GLY | ASN | LYS | CYS | ASP | LEU | PRO | ||||
| 13 | SER | ARG | THR | VAL | ASP | THR | LYS | GLN | ALA | GLN | ||||
| 14 | ASP | LEU | ALA | ARG | SER | TYR | GLY | ILE | PRO | PHE | ||||
| 15 | ILE | GLU | THR | SER | ALA | LYS | THR | ARG | GLN | GLY | ||||
| 16 | VAL | ASP | ASP | ALA | PHE | TYR | THR | LEU | VAL | ARG | ||||
| 17 | GLU | ILE | ARG | LYS | HIS | LYS | GLU | LYS | MET | SER | ||||
| 18 | LYS | ASP | GLY | LYS | LYS | LYS | LYS | LYS | LYS | SER | ||||
| 19 | LYS | THR | LYS | CYS |
Entity 3, entity_3, 1 - C44 H85 N O8 P - 787.121 Da.
| 1 | PCW |
Entity 4, entity_4, 1 - C42 H78 N O10 P - 788.043 Da.
| 1 | 17F |
Entity 5, entity_5, 1 - C10 H15 N5 O11 P2 - 443.201 Da.
| 1 | GDP |
Entity 6, entity_6, 1 - Mg - 24.305 Da.
| 1 | MG |
Samples:
sample_1: KRAS4B, [ILV 13C-methyl; Lys 15N-amide], 80 uM
sample_conditions_1: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-13C TROSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TopSpin, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking, processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis
HADDOCK, Bonvin - refinement, structure calculation
NMR spectrometers:
- Bruker AVANCE III 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts