BMRB Entry 52009

Name: Full assignment of 13C,15N-labeled oncogenic mutant human KRas4B-G12C(1-169) bound to GDP and free of Mg2+ ion at physiological pH
Published: 2023-07-02

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52009

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Full assignment of 13C,15N-labeled oncogenic mutant human KRas4B-G12C(1-169) bound to GDP and free of Mg2+ ion at physiological pH

Deposition date:

2023-06-28

Original release date:

2023-07-02

Authors:

Gadanecz, Marton; Palfy, Gyula; Perczel, Andras

Citation:

Citation: Gadanecz, Marton; Fazekas, Zsolt; Palfy, Gyula; Menyhard, Dora; Perczel, Andras. "NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the Mg2+ Ion" Int. J. Mol. Sci. 24, 12101-12101 (2023).
PubMed: 37569478

Assembly members:

Assembly members:
entity_1, polymer, 169 residues, Formula weight is not available
entity_GDP, non-polymer, 443.201 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MTEYKLVVVGACGVGKSALT IQLIQNHFVDEYDPTIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHHYREQI KRVKDSEDVPMVLVGNKCDL PSRTVDTKQAQDLARSYGIP FIETSAKTRQGVDDAFYTLV REIRKHKEK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	463
15N chemical shifts	158
1H chemical shifts	906

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	KRAS-G12C	1
2	GDP	2

Entities:

Entity 1, KRAS-G12C 169 residues - Formula weight is not available

1

MET

THR

GLU

TYR

LYS

LEU

VAL

GLY

2

ALA

CYS

GLY

VAL

GLY

LYS

SER

ALA

LEU

THR

3

ILE

GLN

LEU

ILE

GLN

ASN

HIS

PHE

VAL

ASP

4

GLU

TYR

ASP

PRO

THR

ILE

GLU

ASP

SER

TYR

5

ARG

LYS

GLN

VAL

ILE

ASP

GLY

GLU

THR

6

CYS

LEU

ASP

ILE

LEU

ASP

THR

ALA

GLY

7

GLN

GLU

TYR

SER

ALA

MET

ARG

ASP

GLN

8

TYR

MET

ARG

THR

GLY

GLU

GLY

PHE

LEU

CYS

9

VAL

PHE

ALA

ILE

ASN

THR

LYS

SER

PHE

10

GLU

ASP

ILE

HIS

TYR

ARG

GLU

GLN

ILE

11

LYS

ARG

VAL

LYS

ASP

SER

GLU

ASP

VAL

PRO

12

MET

VAL

LEU

VAL

GLY

ASN

LYS

CYS

ASP

LEU

13

PRO

SER

ARG

THR

VAL

ASP

THR

LYS

GLN

ALA

14

GLN

ASP

LEU

ALA

ARG

SER

TYR

GLY

ILE

PRO

15

PHE

ILE

GLU

THR

SER

ALA

LYS

THR

ARG

GLN

16

GLY

VAL

ASP

ALA

PHE

TYR

THR

LEU

VAL

17

ARG

GLU

ILE

ARG

LYS

HIS

LYS

GLU

LYS

Entity 2, GDP - C10 H15 N5 O11 P2 - 443.201 Da.

1

GDP

Samples:

sample_1: KRas4b G12C(1-169), [U-99% 13C; U-99% 15N], 0.85 mM; D2O, [U-100% 15N], 7%; DSS 1%; EDTA 10 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; Na2HPO4 10 mM; KH2PO4 1.8 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
4D HC(CC-TOCSY(CO))NH	sample_1	isotropic	sample_conditions_1
4D 13C, 15N-edited SOFAST-HMQC-NOESY-SOFAST-HMQC (HCNH)	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - collection, peak picking, processing

4D-CHAINS - chemical shift assignment

SPARKY - chemical shift assignment

CS-Rosetta - structure solution

GROMACS v2022.2 - refinement

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 700 MHz
Bruker AVANCE NEO 900 MHz