BMRB Entry 30403

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

Data sets:
Data typeCount
13C chemical shifts25
15N chemical shifts84
1H chemical shifts159

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_2, 12
4entity_3, 13
5entity_3, 23
6entity_3, 33
7entity_3, 43
8entity_3, 53
9entity_3, 63
10entity_3, 73
11entity_3, 83
12entity_3, 93
13entity_3, 103
14entity_3, 113
15entity_3, 123
16entity_3, 133
17entity_3, 143
18entity_3, 153
19entity_3, 163
20entity_3, 173
21entity_3, 183
22entity_3, 193
23entity_3, 203
24entity_3, 213
25entity_3, 223
26entity_3, 233
27entity_3, 243
28entity_3, 253
29entity_3, 263
30entity_3, 273
31entity_3, 283
32entity_3, 293
33entity_3, 303
34entity_3, 313
35entity_3, 323
36entity_3, 333
37entity_3, 343
38entity_3, 353
39entity_3, 363
40entity_3, 373
41entity_3, 383
42entity_3, 393
43entity_3, 403
44entity_3, 413
45entity_3, 423
46entity_3, 433
47entity_3, 443
48entity_3, 453
49entity_3, 463
50entity_3, 473
51entity_3, 483
52entity_3, 493
53entity_3, 503
54entity_3, 513
55entity_3, 523
56entity_3, 533
57entity_3, 543
58entity_3, 553
59entity_3, 563
60entity_3, 573
61entity_3, 583
62entity_3, 593
63entity_3, 603
64entity_3, 613
65entity_3, 623
66entity_3, 633
67entity_3, 643
68entity_4, 14
69entity_4, 24
70entity_4, 34
71entity_4, 44
72entity_4, 54
73entity_4, 64
74entity_4, 74
75entity_4, 84
76entity_4, 94
77entity_4, 104
78entity_4, 114
79entity_4, 124
80entity_4, 134
81entity_4, 144
82entity_4, 154
83entity_4, 164
84entity_5, 15
85entity_6, 16
86entity_7, 17

Entities:

Entity 1, entity_1, 1 200 residues - 23234.295 Da.

1   GLYPROLEULYSLEULEUASPASNTRPASP
2   SERVALTHRSERTHRPHESERLYSLEUARG
3   GLUGLNLEUGLYPROVALTHRGLNGLUPHE
4   TRPASPASNLEUGLULYSGLUTHRGLUGLY
5   LEUARGGLNGLUMETSERLYSASPLEUGLU
6   GLUVALLYSALALYSVALGLNPROTYRLEU
7   ASPASPPHEGLNLYSLYSTRPGLNGLUGLU
8   METGLULEUTYRARGGLNLYSVALGLUPRO
9   LEUARGALAGLULEUGLNGLUGLYALAARG
10   GLNLYSLEUHISGLULEUGLNGLULYSLEU
11   SERPROLEUGLYGLUGLUMETARGASPARG
12   ALAARGALAHISVALASPALALEUARGTHR
13   HISLEUALAPROTYRSERASPGLULEUARG
14   GLNARGLEUALAALAARGLEUGLUALALEU
15   LYSGLUASNGLYGLYALAARGLEUALAGLU
16   TYRHISALALYSALATHRGLUHISLEUSER
17   THRLEUSERGLULYSALALYSPROALALEU
18   GLUASPLEUARGGLNGLYLEULEUPROVAL
19   LEUGLUSERPHELYSVALSERPHELEUSER
20   ALALEUGLUGLUTYRTHRLYSLYSLEUASN

Entity 2, entity_2, 1 187 residues - 21302.330 Da.

1   GLYSERMETTHRGLUTYRLYSLEUVALVAL
2   VALGLYALAVALGLYVALGLYLYSSERALA
3   LEUTHRILEGLNLEUILEGLNASNHISPHE
4   VALASPGLUTYRASPPROTHRILEGLUASP
5   SERTYRARGLYSGLNVALVALILEASPGLY
6   GLUTHRCYSLEULEUASPILELEUASPTHR
7   ALAGLYGLNGLUGLUTYRSERALAMETARG
8   ASPGLNTYRMETARGTHRGLYGLUGLYPHE
9   LEUCYSVALPHEALAILEASNASNTHRLYS
10   SERPHEGLUASPILEHISHISTYRARGGLU
11   GLNILELYSARGVALLYSASPSERGLUASP
12   VALPROMETVALLEUVALGLYASNLYSCYS
13   ASPLEUPROSERARGTHRVALASPTHRLYS
14   GLNALAGLNASPLEUALAARGSERTYRGLY
15   ILEPROPHEILEGLUTHRSERALALYSTHR
16   ARGGLNGLYVALASPASPALAPHETYRTHR
17   LEUVALARGGLUILEARGLYSHISLYSGLU
18   LYSMETSERLYSASPGLYLYSLYSLYSLYS
19   LYSLYSSERLYSTHRLYSCYS

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:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1
2D 1H-13C HMQCsample_2isotropicsample_conditions_1
2D 1H-13C HMQCsample_1isotropicsample_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