BMRBj - BMREntryMaster

Found 1 Document (3.524 seconds)

BMRB: 25116

2MSE

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

Authors

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

Assembly

GTPase KRas-GNP:ARafRBD complex

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

3. A-RafRBD (polymer), 73 monomers, 8122.398 Da Detail

GTVKVYLPNK QRTVVTVRDG MSVYDSLDKA LKVRGLNQDC CVVYRLIKGR KTVTAWDTAI APLDGEELIV EVL

Total weight

52545.277 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: 4.6 %, Completeness: 1.4 %, Completeness (bb): 1.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	1.4 % (70 of 4972)	1.2 % (35 of 2860)	1.7 % (35 of 2112)
Backbone	1.1 % (25 of 2286)	1.0 % (9 of 932)	1.2 % (16 of 1354)
Sidechain	1.6 % (51 of 3120)	1.3 % (26 of 1928)	2.1 % (25 of 1192)
Aromatic	0.0 % (0 of 318)	0.0 % (0 of 161)	0.0 % (0 of 157)
Methyl	7.7 % (40 of 518)	8.1 % (21 of 259)	7.3 % (19 of 259)

1. K-Ras

2. membrane scaffold protein

3. A-RafRBD

GTVKVYLPNK QRTVVTVRDG MSVYDSLDKA LKVRGLNQDC CVVYRLIKGR KTVTAWDTAI APLDGEELIV EVL

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	K-Ras	U-15N, Ile C-delta-13C	0.6 mM
2	membrane scaffold protein	natural abundance	0.6 mM
3	A-RafRBD	natural abundance	0.7 mM
4	sodium chloride	natural abundance	100 mM
5	Magnesium	natural abundance	5 mM
6	TRIS	natural abundance	20 mM
7	TCEP	natural abundance	2 mM
8	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.6 mM
9	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
10	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
11	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	Concentration
12	K-Ras	natural abundance	0.7 mM
13	membrane scaffold protein	natural abundance	0.7 mM
14	A-RafRBD	U-15N, Ile C-delta-13C	0.6 mM
15	Magnesium	natural abundance	5 mM
16	TRIS	natural abundance	20 mM
17	sodium chloride	natural abundance	100 mM
18	TCEP	natural abundance	2 mM
19	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.7 mM
20	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
21	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
22	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM

Sample #3

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

#	Name	Isotope labeling	Concentration
23	K-Ras	U-15N, Ile C-delta-13C	0.6 mM
24	A-RafRBD	natural abundance	0.7 mM
25	membrane scaffold protein	natural abundance	0.6 mM
26	TRIS	natural abundance	20 mM
27	sodium chloride	natural abundance	100 mM
28	Magnesium	natural abundance	5 mM
29	TCEP	natural abundance	2 mM
30	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.6 mM
31	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
32	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
33	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM
34	1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)	natural abundance	0.65 mM

Sample #4

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

#	Name	Isotope labeling	Concentration
35	K-Ras	natural abundance	0.7 mM
36	A-RafRBD	U-15N, Ile C-delta-13C	0.6 mM
37	membrane scaffold protein	natural abundance	0.7 mM
38	TRIS	natural abundance	20 mM
39	sodium chloride	natural abundance	100 mM
40	Magnesium	natural abundance	5 mM
41	TCEP	natural abundance	2 mM
42	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.7 mM
43	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
44	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
45	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM
46	1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)	natural abundance	0.65 mM

Protein Blocks Logo

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

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

Related entities 3. A-RafRBD, : 1 : 6 : 2 : 67 entities Detail

Interaction partners 3. A-RafRBD, : 59 interactors Detail

More details for 59 interactors identified by 25 citations

Experiments performed 4 experiments Detail

1 2D 1H-13C HMQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	K-Ras	U-15N, Ile C-delta-13C	0.6 mM
2	membrane scaffold protein	natural abundance	0.6 mM
3	A-RafRBD	natural abundance	0.7 mM
4	sodium chloride	natural abundance	100 mM
5	Magnesium	natural abundance	5 mM
6	TRIS	natural abundance	20 mM
7	TCEP	natural abundance	2 mM
8	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.6 mM
9	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
10	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
11	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM

2 2D 1H-13C HMQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
12	K-Ras	natural abundance	0.7 mM
13	membrane scaffold protein	natural abundance	0.7 mM
14	A-RafRBD	U-15N, Ile C-delta-13C	0.6 mM
15	Magnesium	natural abundance	5 mM
16	TRIS	natural abundance	20 mM
17	sodium chloride	natural abundance	100 mM
18	TCEP	natural abundance	2 mM
19	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.7 mM
20	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
21	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
22	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM

3 2D 1H-13C HMQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
23	K-Ras	U-15N, Ile C-delta-13C	0.6 mM
24	A-RafRBD	natural abundance	0.7 mM
25	membrane scaffold protein	natural abundance	0.6 mM
26	TRIS	natural abundance	20 mM
27	sodium chloride	natural abundance	100 mM
28	Magnesium	natural abundance	5 mM
29	TCEP	natural abundance	2 mM
30	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.6 mM
31	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
32	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
33	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM
34	1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)	natural abundance	0.65 mM

4 2D 1H-13C HMQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
35	K-Ras	natural abundance	0.7 mM
36	A-RafRBD	U-15N, Ile C-delta-13C	0.6 mM
37	membrane scaffold protein	natural abundance	0.7 mM
38	TRIS	natural abundance	20 mM
39	sodium chloride	natural abundance	100 mM
40	Magnesium	natural abundance	5 mM
41	TCEP	natural abundance	2 mM
42	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	0.7 mM
43	1,2-dioleoyl-sn-glycero-3-phosphocholine	natural abundance	18.75 mM
44	1,2-dioleoyl-sn-glycero-3-phospho-L-serine	natural abundance	5 mM
45	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]	natural abundance	1.25 mM
46	1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)	natural abundance	0.65 mM

nullKeywords A-RafRBD, Docking, K-Ras, Nanodisc, PRE

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (3.524 seconds)

BMRB: 25116

Sample #1

Sample #2

Sample #3

Sample #4

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

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

Related entities 3. A-RafRBD, : 1 : 6 : 2 : 67 entities Detail

Interaction partners 3. A-RafRBD, : 59 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample