BMRB: 25115

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

Authors

Mazhab-Jafari, M., Stathopoulos, P., Marshall, C., Ikura, M.

Assembly

K-Ras and membrane scaffold protein

Entity

1. K-Ras (polymer), 187 monomers, 21224.93 Da Detail

GSMTEYKLVV VGAGGVGKSA LTIQLIQNHF VDEYDPTIED SYRKQVVIDG ETCLLDILDT AGQEEYSAMR DQYMRTGEGF LCVFAINNTK SFEDIHHYRE QIKRVKDSED VPMVLVGNKC DLPSRTVDTK QAQDLARSYG IPFIETSAKT RQGVDDAFYT LVREIRKHKE KMSKDGKKKK KKSKTKC

2. membrane scaffold protein (polymer, Thiol state: not present), 200 monomers, 23197.95 Da Detail

GPLKLLDNWD SVTSTFSKLR EQLGPVTQEF WDNLEKETEG LRQEMSKDLE EVKAKVQPYL DDFQKKWQEE MELYRQKVEP LRAELQEGAR QKLHELQEKL SPLGEEMRDR ARAHVDALRT HLAPYSDELR QRLAARLEAL KENGGARLAE YHAKATEHLS TLSEKAKPAL EDLRGELLPV LESFKVSFLS ALEEYTKKLN

Total weight

44422.88 Da

Max. entity weight

23197.95 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 7.0 %, Completeness: 2.2 %, Completeness (bb): 2.2 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
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• TSV

Polymer type: polypeptide(L)

	Total	1H	13C
All	2.2 % (94 of 4205)	2.4 % (58 of 2426)	2.0 % (36 of 1779)
Backbone	2.2 % (43 of 1923)	3.1 % (24 of 783)	1.7 % (19 of 1140)
Sidechain	2.2 % (58 of 2648)	2.2 % (36 of 1643)	2.2 % (22 of 1005)
Aromatic	0.0 % (0 of 283)	0.0 % (0 of 143)	0.0 % (0 of 140)
Methyl	5.9 % (24 of 406)	6.4 % (13 of 203)	5.4 % (11 of 203)

1. K-Ras

GSMTEYKLVV VGAGGVGKSA LTIQLIQNHF VDEYDPTIED SYRKQVVIDG ETCLLDILDT AGQEEYSAMR DQYMRTGEGF LCVFAINNTK SFEDIHHYRE QIKRVKDSED VPMVLVGNKC DLPSRTVDTK QAQDLARSYG IPFIETSAKT RQGVDDAFYT LVREIRKHKE KMSKDGKKKK KKSKTKC

2. membrane scaffold protein

GPLKLLDNWD SVTSTFSKLR EQLGPVTQEF WDNLEKETEG LRQEMSKDLE EVKAKVQPYL DDFQKKWQEE MELYRQKVEP LRAELQEGAR QKLHELQEKL SPLGEEMRDR ARAHVDALRT HLAPYSDELR QRLAARLEAL KENGGARLAE YHAKATEHLS TLSEKAKPAL EDLRGELLPV LESFKVSFLS ALEEYTKKLN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	K-Ras	U-15N, Ile C-delta-13C		0.6 mM
2	membrane scaffold protein	natural abundance		0.6 mM
3	TRIS	natural abundance		20 mM
4	sodium chloride	natural abundance		100 mM
5	TCEP	natural abundance		2 mM
6	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance		0.6 mM
7	Magnesium	natural abundance		5 mM
8	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance		18.75 mM
9	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance		5 mM
10	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance		1.25 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
11	K-Ras	U-15N, Ile C-delta-13C		0.6 mM
12	membrane scaffold protein	natural abundance		0.6 mM
13	TRIS	natural abundance		20 mM
14	sodium chloride	natural abundance		100 mM
15	Magnesium	natural abundance		5 mM
16	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance		0.6 mM
17	TCEP	natural abundance		2 mM
18	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance		18.75 mM
19	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance		5 mM
20	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance		1.25 mM
21	1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)	natural abundance		0.65 mM

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Protein Blocks Logo

Calculated from 10 models in PDB: 2MSD, Strand ID: A, B, C Detail

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Release date

2015-05-26

Citation

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site
Mazhab-Jafari, M., Marshall, C., Smith, M., Gasmi-Seabrook, G., Stathopoulos, P., Inagaki, F., Kay, L., Neel, B., Ikura, M.
Proc. Natl. Acad. Sci. U. S. A. (2015), 112, 6625-6630, PubMed 25941399 , DOI 10.1073/pnas.1419895112 , Abstract

Related entities 1. K-Ras, : 101 entities Detail

Related entities 2. membrane scaffold protein, : 1 : 18 : 31 entities Detail

Experiments performed 2 experiments Detail