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BMRB: 30640

1AV1

NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state B)

Authors

Fang, Z., Lee, K., Gasmi-Seabrook, G., Ikura, M., Marshall, C.B.

Assembly

Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase

Entity

1. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 1 (polymer), 198 monomers, 23042.79 × 2 Da Detail

LKLLDNWDSV TSTFSKLREQ LGPVTQEFWD NLEKETEGLR QEMSKDLEEV KAKVQPYLDD FQKKWQEEME LYRQKVEPLR AELQEGARQK LHELQEKLSP LGEEMRDRAR AHVDALRTHL APYSDELRQR LAARLEALKE NGGARLAEYH AKATEHLSTL SEKAKPALED LRQGLLPVLE SFKVSFLSAL EEYTKKLN

2. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 2 (polymer), 185 monomers, 21080.80 Da Detail

MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPTIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ YMRTGEGFLC VFAINNTKSF EDIHHYREQI KRVKDSEDVP MVLVGNKCDL PSRTVDTKQA QDLARSYGIP FIETSAKTRQ GVDDAFYTLV REIRKHKEKM SKDGKKKKKK SKTKC

3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3 (polymer), 132 monomers, 15241.71 Da Detail

NTIRVFLPNK QRTVVNVRNG MSLHDCLMKA LKVRGLQPEC CAVFRLLQEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DW

4. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity PCW (non-polymer), 787.121 × 64 Da
5. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 17F (non-polymer), 788.043 × 15 Da
6. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity GNP (non-polymer), 522.196 Da
7. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity MG (non-polymer), 24.305 Da
8. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

145281.8 Da

Max. entity weight

23042.79 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 42.5 %, Completeness: 10.5 %, Completeness (bb): 16.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	10.5 % (650 of 6176)	9.8 % (316 of 3241)	5.1 % (122 of 2388)	38.8 % (212 of 547)
Backbone	16.1 % (494 of 3060)	21.5 % (224 of 1040)	3.8 % (58 of 1520)	42.4 % (212 of 500)
Sidechain	4.9 % (176 of 3606)	4.2 % (92 of 2201)	6.2 % (84 of 1358)	0.0 % (0 of 47)
Aromatic	1.9 % (8 of 432)	1.9 % (4 of 216)	1.9 % (4 of 211)	0.0 % (0 of 5)
Methyl	16.6 % (92 of 554)	15.9 % (44 of 277)	17.3 % (48 of 277)

1. entity 1

2. entity 2

3. entity 3

NTIRVFLPNK QRTVVNVRNG MSLHDCLMKA LKVRGLQPEC CAVFRLLQEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H] KRAS, 0.2 mM [U-12C; U-14N; U-1H] RBD-CRD, 0.4 mM [U-12C; U-14N; U-1H] MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KRAS	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
2	RBD-CRD	[U-12C; U-14N; U-1H]	0.2 mM
3	MSP	[U-12C; U-14N; U-1H]	0.4 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [U-12C; U-14N; U-1H] KRAS, 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H] RBD-CRD, 0.4 mM [U-12C; U-14N; U-1H] MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C; U-14N; U-1H]	0.2 mM
5	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
6	MSP	[U-12C; U-14N; U-1H]	0.4 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N] RBD-CRD, 0.2 mM [U-12C; U-14N; U-1H] KRAS Q43C, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
8	KRAS Q43C	[U-12C; U-14N; U-1H]		0.2 mM

Sample #4

#	Name	Isotope labeling	Type	Concentration
9	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
10	KRAS N-term C	[U-12C; U-14N; U-1H]		0.2 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-15N; Ile C-delta-13C; Met methyl-13C] KRAS, 0.5 mM [Leu C-delta-13C; Val C-gamma-13C] RBD-CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	KRAS	[U-15N; Ile C-delta-13C; Met methyl-13C]		0.5 mM
12	RBD-CRD	[Leu C-delta-13C; Val C-gamma-13C]		0.5 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-13C; U-15N] RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-13C; U-15N]		0.5 mM

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-13C; U-15N] CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-13C; U-15N]		0.5 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 6PTW, Strand ID: A, B, C, D Detail

Release date

2019-08-15

Citation

Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane
Fang, Z., Lee, K.Y., Huo, K.G., Gasmi-Seabrook, G., Zheng, L., Moghal, N., Tsao, M.S., Ikura, M., Marshall, C.B.
Proc. Natl. Acad. Sci. U. S. A. (2020), 117, 12101-12108, PubMed 32414921 , DOI 10.1073/pnas.1914076117 , Abstract

Related entities 1. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 1, : 1 : 15 : 3 : 30 entities Detail

Related entities 2. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 2, : 100 entities Detail

Related entities 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 6 : 14 : 38 entities Detail

Interaction partners 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 19 interactors Detail

More details for 19 interactors identified by 12 citations

Experiments performed 21 experiments Detail

1 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H] KRAS, 0.2 mM [U-12C; U-14N; U-1H] RBD-CRD, 0.4 mM [U-12C; U-14N; U-1H] MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KRAS	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
2	RBD-CRD	[U-12C; U-14N; U-1H]	0.2 mM
3	MSP	[U-12C; U-14N; U-1H]	0.4 mM

2 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	KRAS	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
2	RBD-CRD	[U-12C; U-14N; U-1H]	0.2 mM
3	MSP	[U-12C; U-14N; U-1H]	0.4 mM

3 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [U-12C; U-14N; U-1H] KRAS, 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H] RBD-CRD, 0.4 mM [U-12C; U-14N; U-1H] MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C; U-14N; U-1H]	0.2 mM
5	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
6	MSP	[U-12C; U-14N; U-1H]	0.4 mM

4 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C; U-14N; U-1H]	0.2 mM
5	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N; U-2H]	0.2 mM
6	MSP	[U-12C; U-14N; U-1H]	0.4 mM

5 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM [Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N] RBD-CRD, 0.2 mM [U-12C; U-14N; U-1H] KRAS Q43C, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
8	KRAS Q43C	[U-12C; U-14N; U-1H]		0.2 mM

6 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
10	KRAS N-term C	[U-12C; U-14N; U-1H]		0.2 mM

7 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
8	KRAS Q43C	[U-12C; U-14N; U-1H]		0.2 mM

8 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	RBD-CRD	[Ile, Leu C-delta-13C; Val C-gamma-13C; U-15N]		0.2 mM
10	KRAS N-term C	[U-12C; U-14N; U-1H]		0.2 mM

9 3D edited NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 0.5 mM [U-15N; Ile C-delta-13C; Met methyl-13C] KRAS, 0.5 mM [Leu C-delta-13C; Val C-gamma-13C] RBD-CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	KRAS	[U-15N; Ile C-delta-13C; Met methyl-13C]		0.5 mM
12	RBD-CRD	[Leu C-delta-13C; Val C-gamma-13C]		0.5 mM

10 3D HNCO