BMRB Entry 30403

Name: NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc
Published: 2018-08-20

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PDB ID: 6ccx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30403
MolProbity Validation Chart

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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 data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc

Deposition date:

2018-02-07

Original release date:

2018-08-20

Authors:

Fang, Z.; Marshall, C.; Nishikawa, T.; Gossert, A.; Jansen, J.; Jahnke, W.; Ikura, M.

Citation:

Citation: Fang, Z.; Marshall, C.; Nishikawa, T.; Gossert, A.; Jansen, J.; Jahnke, W.; Ikura, M.. "Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site" Cell Chem. Biol. 25, 1327-11336 (2018).
PubMed: 30122370

Assembly members:

Assembly members:
entity_1, polymer, 200 residues, 23234.295 Da.
entity_2, polymer, 187 residues, 21302.330 Da.
entity_PCW, non-polymer, 787.121 Da.
entity_17F, non-polymer, 788.043 Da.
entity_GNP, non-polymer, 522.196 Da.
entity_MG, non-polymer, 24.305 Da.
entity_EWS, non-polymer, 446.768 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLKLLDNWDSVTSTFSKLR EQLGPVTQEFWDNLEKETEG LRQEMSKDLEEVKAKVQPYL DDFQKKWQEEMELYRQKVEP LRAELQEGARQKLHELQEKL SPLGEEMRDRARAHVDALRT HLAPYSDELRQRLAARLEAL KENGGARLAEYHAKATEHLS TLSEKAKPALEDLRQGLLPV LESFKVSFLSALEEYTKKLN
entity_2: GSMTEYKLVVVGAVGVGKSA LTIQLIQNHFVDEYDPTIED SYRKQVVIDGETCLLDILDT AGQEEYSAMRDQYMRTGEGF LCVFAINNTKSFEDIHHYRE QIKRVKDSEDVPMVLVGNKC DLPSRTVDTKQAQDLARSYG IPFIETSAKTRQGVDDAFYT LVREIRKHKEKMSKDGKKKK KKSKTKC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	25
15N chemical shifts	84
1H chemical shifts	159

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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_3, 1	3
5	entity_3, 2	3
6	entity_3, 3	3
7	entity_3, 4	3
8	entity_3, 5	3
9	entity_3, 6	3
10	entity_3, 7	3
11	entity_3, 8	3
12	entity_3, 9	3
13	entity_3, 10	3
14	entity_3, 11	3
15	entity_3, 12	3
16	entity_3, 13	3
17	entity_3, 14	3
18	entity_3, 15	3
19	entity_3, 16	3
20	entity_3, 17	3
21	entity_3, 18	3
22	entity_3, 19	3
23	entity_3, 20	3
24	entity_3, 21	3
25	entity_3, 22	3
26	entity_3, 23	3
27	entity_3, 24	3
28	entity_3, 25	3
29	entity_3, 26	3
30	entity_3, 27	3
31	entity_3, 28	3
32	entity_3, 29	3
33	entity_3, 30	3
34	entity_3, 31	3
35	entity_3, 32	3
36	entity_3, 33	3
37	entity_3, 34	3
38	entity_3, 35	3
39	entity_3, 36	3
40	entity_3, 37	3
41	entity_3, 38	3
42	entity_3, 39	3
43	entity_3, 40	3
44	entity_3, 41	3
45	entity_3, 42	3
46	entity_3, 43	3
47	entity_3, 44	3
48	entity_3, 45	3
49	entity_3, 46	3
50	entity_3, 47	3
51	entity_3, 48	3
52	entity_3, 49	3
53	entity_3, 50	3
54	entity_3, 51	3
55	entity_3, 52	3
56	entity_3, 53	3
57	entity_3, 54	3
58	entity_3, 55	3
59	entity_3, 56	3
60	entity_3, 57	3
61	entity_3, 58	3
62	entity_3, 59	3
63	entity_3, 60	3
64	entity_3, 61	3
65	entity_3, 62	3
66	entity_3, 63	3
67	entity_3, 64	3
68	entity_4, 1	4
69	entity_4, 2	4
70	entity_4, 3	4
71	entity_4, 4	4
72	entity_4, 5	4
73	entity_4, 6	4
74	entity_4, 7	4
75	entity_4, 8	4
76	entity_4, 9	4
77	entity_4, 10	4
78	entity_4, 11	4
79	entity_4, 12	4
80	entity_4, 13	4
81	entity_4, 14	4
82	entity_4, 15	4
83	entity_4, 16	4
84	entity_5, 1	5
85	entity_6, 1	6
86	entity_7, 1	7

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, 1 187 residues - 21302.330 Da.

1

GLY

SER

MET

THR

GLU

TYR

LYS

LEU

VAL

2

VAL

GLY

ALA

VAL

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 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 H17 N6 O13 P3 - 522.196 Da.

1

GNP

Entity 6, entity_6, 1 - Mg - 24.305 Da.

1

MG

Entity 7, entity_7, 1 - C21 H21 Br Cl N3 O - 446.768 Da.

1

EWS

Samples:

sample_1: GTPase KRas isoform b, U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C, 0.2 mM; Membrane Scaffold Protein 0.4 mM; sodium chloride 100 mM; TRIS 20 mM; magnesium chloride 5 mM; TCEP 2 mM; GMPPNP 0.2 mM; DOPC 12 mM; DOPS 3.2 mM; PE-MCC 0.8 mM

sample_2: GTPase KRas isoform b 0.2 mM; Membrane Scaffold Protein 0.4 mM; sodium chloride 100 mM; TRIS 20 mM; magnesium chloride 5 mM; TCEP 2 mM; GMPPNP 0.2 mM; DOPC 12 mM; DOPS 3.2 mM; PE-MCC 0.8 mM; PE-DTPA-Gd 0.4 mM

sample_conditions_1: ionic strength: 105 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - data analysis

HADDOCK, Bonvin - refinement, structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AvanceII 800 MHz

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

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

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

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