BMRB Entry 51071

Name: NMR-driven structure of KRAS4B-G12D-GTP homodimer on a lipid bilayer nanodisc
Published: 2021-11-01

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51071

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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:

NMR-driven structure of KRAS4B-G12D-GTP homodimer on a lipid bilayer nanodisc

Deposition date:

2021-08-26

Original release date:

2021-11-01

Authors:

Lee, Ki-Young; Enomoto, Masahiro; Gebregiworgis, Teklab; Gasmi-Seabrook, Genevieve; Ikura, Mitsuhiko; Marshall, Christopher

Citation:

Citation: Lee, Ki-Young; Enomoto, Masahiro; Gebregiworgis, Teklab; Gasmi-Seabrook, Genevieve; Ikura, Mitsuhiko; Marshall, Christopher. "Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization" Chem. Sci. 12, 12827-12837 (2021).
PubMed: 34703570

Assembly members:

Assembly members:
entity_1, polymer, 185 residues, Formula weight is not available
entity_GTP, non-polymer, 523.180 Da.
entity_MG, non-polymer, 24.305 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MTEYKLVVVGADGVGKSALT IQLIQNHFVDEYDPTIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHHYREQI KRVKDSEDVPMVLVGNKCDL PSRTVDTKQAQDLARSYGIP FIETSAKTRQGVDDAFYTLV REIRKHKEKMSKDGKKKKKK SKTKC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	30
15N chemical shifts	15
1H chemical shifts	105

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	KRAS4B-G12D	1
2	GTP	2
3	MG ion	3

Entities:

Entity 1, KRAS4B-G12D 185 residues - Formula weight is not available

1

MET

THR

GLU

TYR

LYS

LEU

VAL

GLY

2

ALA

ASP

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

MET

18

SER

LYS

ASP

GLY

LYS

19

SER

LYS

THR

LYS

CYS

Entity 2, GTP - C10 H16 N5 O14 P3 - 523.180 Da.

1

GTP

Entity 3, MG ion - Mg - 24.305 Da.

1

MG

Samples:

sample_1: KRAS4B-G12D, ILV 13C-methyl / K 15N-amide, 80 uM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.4; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1

Software:

NMRViewJ - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks