BMRB Entry 25116

Name: NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc
Published: 2015-05-27

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PDB ID: 2mse
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25116
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc

Deposition date:

2014-07-29

Original release date:

2015-05-27

Authors:

Mazhab-Jafari, Mohammad T.; Stathopoulos, Peter B.; Marshall, Christopher B.; Ikura, Mitsuhiko

Citation:

Citation: Mazhab-Jafari, Mohammad T.; Marshall, Christopher B.; Smith, Matthew J.; Gasmi-Seabrook, Genevieve M. C.; Stathopoulos, Peter B.; Inagaki, Fuyuhiko; Kay, Lewis E.; Neel, Benjamin G.; Ikura, Mitsuhiko. "Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site" Proc. Natl. Acad. Sci. U. S. A. 112, 6625-6630 (2015).
PubMed: 25941399

Assembly members:

Assembly members:
K-Ras, polymer, 187 residues, 8696.952 Da.
membrane_scaffold_protein, polymer, 200 residues, 63628.461 Da.
A-RafRBD, polymer, 73 residues, Formula weight is not available

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: pET-28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
K-Ras: GSMTEYKLVVVGAGGVGKSA LTIQLIQNHFVDEYDPTIED SYRKQVVIDGETCLLDILDT AGQEEYSAMRDQYMRTGEGF LCVFAINNTKSFEDIHHYRE QIKRVKDSEDVPMVLVGNKC DLPSRTVDTKQAQDLARSYG IPFIETSAKTRQGVDDAFYT LVREIRKHKEKMSKDGKKKK KKSKTKC
membrane_scaffold_protein: GPLKLLDNWDSVTSTFSKLR EQLGPVTQEFWDNLEKETEG LRQEMSKDLEEVKAKVQPYL DDFQKKWQEEMELYRQKVEP LRAELQEGARQKLHELQEKL SPLGEEMRDRARAHVDALRT HLAPYSDELRQRLAARLEAL KENGGARLAEYHAKATEHLS TLSEKAKPALEDLRGELLPV LESFKVSFLSALEEYTKKLN
A-RafRBD: GTVKVYLPNKQRTVVTVRDG MSVYDSLDKALKVRGLNQDC CVVYRLIKGRKTVTAWDTAI APLDGEELIVEVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	13
1H chemical shifts	39

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	K-Ras	1
2	membrane scaffold protein	2
3	A-RafRBD	3

Entities:

Entity 1, K-Ras 187 residues - 8696.952 Da.

1

GLY

SER

MET

THR

GLU

TYR

LYS

LEU

VAL

2

VAL

GLY

ALA

GLY

VAL

GLY

LYS

SER

ALA

3

LEU

THR

ILE

GLN

LEU

ILE

GLN

ASN

HIS

PHE

4

VAL

ASP

GLU

TYR

ASP

PRO

THR

ILE

GLU

ASP

5

SER

TYR

ARG

LYS

GLN

VAL

ILE

ASP

GLY

6

GLU

THR

CYS

LEU

ASP

ILE

LEU

ASP

THR

7

ALA

GLY

GLN

GLU

TYR

SER

ALA

MET

ARG

8

ASP

GLN

TYR

MET

ARG

THR

GLY

GLU

GLY

PHE

9

LEU

CYS

VAL

PHE

ALA

ILE

ASN

THR

LYS

10

SER

PHE

GLU

ASP

ILE

HIS

TYR

ARG

GLU

11

GLN

ILE

LYS

ARG

VAL

LYS

ASP

SER

GLU

ASP

12

VAL

PRO

MET

VAL

LEU

VAL

GLY

ASN

LYS

CYS

13

ASP

LEU

PRO

SER

ARG

THR

VAL

ASP

THR

LYS

14

GLN

ALA

GLN

ASP

LEU

ALA

ARG

SER

TYR

GLY

15

ILE

PRO

PHE

ILE

GLU

THR

SER

ALA

LYS

THR

16

ARG

GLN

GLY

VAL

ASP

ALA

PHE

TYR

THR

17

LEU

VAL

ARG

GLU

ILE

ARG

LYS

HIS

LYS

GLU

18

LYS

MET

SER

LYS

ASP

GLY

LYS

19

LYS

SER

LYS

THR

LYS

CYS

Entity 2, membrane scaffold protein 200 residues - 63628.461 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	GLY	GLU	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 3, A-RafRBD 73 residues - Formula weight is not available

1

GLY

THR

VAL

LYS

VAL

TYR

LEU

PRO

ASN

LYS

2

GLN

ARG

THR

VAL

THR

VAL

ARG

ASP

GLY

3

MET

SER

VAL

TYR

ASP

SER

LEU

ASP

LYS

ALA

4

LEU

LYS

VAL

ARG

GLY

LEU

ASN

GLN

ASP

CYS

5

CYS

VAL

TYR

ARG

LEU

ILE

LYS

GLY

ARG

6

LYS

THR

VAL

THR

ALA

TRP

ASP

THR

ALA

ILE

7

ALA

PRO

LEU

ASP

GLY

GLU

LEU

ILE

VAL

8

GLU

VAL

LEU

Name	Sample	Sample state	Sample conditions
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_4	isotropic	sample_conditions_1

BMRB	17785 18529 25114 25115 26635
PDB	2MSC 2MSD 2MSE 3GFT 4DSN 4DSO 4DST 4DSU 4EPR 4EPT 4EPV 4EPW 4EPX 4EPY 4L8G 4LDJ 4LPK 4LRW 4LUC 4LV6 4LYF 4LYH 4LYJ 4M1O 4M1S 4M1T 4M1W 4M1Y 4M21 4M22 4NMM 4OBE 4PZY 4PZZ 4Q01 4Q02 4Q03 4QL3 4TQ9 4TQA 4WA7
DBJ	BAE33023 BAE37609 BAF85199 BAJ17756
EMBL	CAA25624 CAA26295 CAA37336 CAA59755 CAA76678
GB	AAA35689 AAA35690 AAA36554 AAA42011 AAA49429
PIR	A54321
PRF	0909262B
REF	NP_001003744 NP_001028153 NP_001095209 NP_001103471 NP_001184192
SP	O42277 P79800 Q05147 Q07983 Q5EFX7
TPG	DAA29418
AlphaFold	O42277 P79800 Q05147 Q07983 Q5EFX7 A0A024RAV5 Q9UCT8

BMRB Entry 25116

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

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	GLY	GLU	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

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	GLY	GLU	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

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	GLY	GLU	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