BMRB Entry 30639

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30639
MolProbity Validation Chart

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Title:
NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)
Deposition date:
2019-07-16
Original release date:
2020-05-08
Authors:
Fang, Z.; Lee, K.; Gasmi-Seabrook, G.; Ikura, M.; Marshall, C.
Citation:

Citation: Fang, Zhenhao; Lee, Ki-Young; Huo, Ku-Geng; Gasmi-Seabrook, Genevieve; Zheng, Le; Moghal, Nadeem; Tsao, Ming-Sound; Ikura, Mitsuhiko; Marshall, Christopher. "Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane"  Proc. Natl. Acad. Sci. U. S. A. 117, 12101-12108 (2020).
PubMed: 32414921

Assembly members:

Assembly members:
entity_1, polymer, 198 residues, 23080.129 Da.
entity_2, polymer, 185 residues, 21116.119 Da.
entity_3, polymer, 132 residues, 15266.923 Da.
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, non-polymer, 787.121 Da.
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine, non-polymer, 788.043 Da.
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, non-polymer, 522.196 Da.
MAGNESIUM ION, non-polymer, 24.305 Da.
ZINC ION, non-polymer, 65.409 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: LKLLDNWDSVTSTFSKLREQ LGPVTQEFWDNLEKETEGLR QEMSKDLEEVKAKVQPYLDD FQKKWQEEMELYRQKVEPLR AELQEGARQKLHELQEKLSP LGEEMRDRARAHVDALRTHL APYSDELRQRLAARLEALKE NGGARLAEYHAKATEHLSTL SEKAKPALEDLRQGLLPVLE SFKVSFLSALEEYTKKLN
entity_2: MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPTIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHHYREQI KRVKDSEDVPMVLVGNKCDL PSRTVDTKQAQDLARSYGIP FIETSAKTRQGVDDAFYTLV REIRKHKEKMSKDGKKKKKK SKTKC
entity_3: NTIRVFLPNKQRTVVNVRNG MSLHDCLMKALKVRGLQPEC CAVFRLLQEHKGKKARLDWN TDAASLIGEELQVDFLDHVP LTTHNFARKTFLKLAFCDIC QKFLLNGFRCQTCGYKFHEH CSTKVPTMCVDW

Data sets:
Data typeCount
13C chemical shifts41
15N chemical shifts198
1H chemical shifts318

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_2, 12
4entity_3, 13
5entity_4, 14
6entity_4, 24
7entity_4, 34
8entity_4, 44
9entity_4, 54
10entity_4, 64
11entity_4, 74
12entity_4, 84
13entity_4, 94
14entity_4, 104
15entity_4, 114
16entity_4, 124
17entity_4, 134
18entity_4, 144
19entity_4, 154
20entity_4, 164
21entity_4, 174
22entity_4, 184
23entity_4, 194
24entity_4, 204
25entity_4, 214
26entity_4, 224
27entity_4, 234
28entity_4, 244
29entity_4, 254
30entity_4, 264
31entity_4, 274
32entity_4, 284
33entity_4, 294
34entity_4, 304
35entity_4, 314
36entity_4, 324
37entity_4, 334
38entity_4, 344
39entity_4, 354
40entity_4, 364
41entity_4, 374
42entity_4, 384
43entity_4, 394
44entity_4, 404
45entity_4, 414
46entity_4, 424
47entity_4, 434
48entity_4, 444
49entity_4, 454
50entity_4, 464
51entity_4, 474
52entity_4, 484
53entity_4, 494
54entity_4, 504
55entity_4, 514
56entity_4, 524
57entity_4, 534
58entity_4, 544
59entity_4, 554
60entity_4, 564
61entity_4, 574
62entity_4, 584
63entity_4, 594
64entity_4, 604
65entity_4, 614
66entity_4, 624
67entity_4, 634
68entity_4, 644
69entity_5, 15
70entity_5, 25
71entity_5, 35
72entity_5, 45
73entity_5, 55
74entity_5, 65
75entity_5, 75
76entity_5, 85
77entity_5, 95
78entity_5, 105
79entity_5, 115
80entity_5, 125
81entity_5, 135
82entity_5, 145
83entity_5, 155
84entity_6, 16
85entity_7, 17
86entity_8, 18
87entity_8, 28

Entities:

Entity 1, entity_1, 1 198 residues - 23080.129 Da.

1   LEULYSLEULEUASPASNTRPASPSERVAL
2   THRSERTHRPHESERLYSLEUARGGLUGLN
3   LEUGLYPROVALTHRGLNGLUPHETRPASP
4   ASNLEUGLULYSGLUTHRGLUGLYLEUARG
5   GLNGLUMETSERLYSASPLEUGLUGLUVAL
6   LYSALALYSVALGLNPROTYRLEUASPASP
7   PHEGLNLYSLYSTRPGLNGLUGLUMETGLU
8   LEUTYRARGGLNLYSVALGLUPROLEUARG
9   ALAGLULEUGLNGLUGLYALAARGGLNLYS
10   LEUHISGLULEUGLNGLULYSLEUSERPRO
11   LEUGLYGLUGLUMETARGASPARGALAARG
12   ALAHISVALASPALALEUARGTHRHISLEU
13   ALAPROTYRSERASPGLULEUARGGLNARG
14   LEUALAALAARGLEUGLUALALEULYSGLU
15   ASNGLYGLYALAARGLEUALAGLUTYRHIS
16   ALALYSALATHRGLUHISLEUSERTHRLEU
17   SERGLULYSALALYSPROALALEUGLUASP
18   LEUARGGLNGLYLEULEUPROVALLEUGLU
19   SERPHELYSVALSERPHELEUSERALALEU
20   GLUGLUTYRTHRLYSLYSLEUASN

Entity 2, entity_2, 1 185 residues - 21116.119 Da.

1   METTHRGLUTYRLYSLEUVALVALVALGLY
2   ALAGLYGLYVALGLYLYSSERALALEUTHR
3   ILEGLNLEUILEGLNASNHISPHEVALASP
4   GLUTYRASPPROTHRILEGLUASPSERTYR
5   ARGLYSGLNVALVALILEASPGLYGLUTHR
6   CYSLEULEUASPILELEUASPTHRALAGLY
7   GLNGLUGLUTYRSERALAMETARGASPGLN
8   TYRMETARGTHRGLYGLUGLYPHELEUCYS
9   VALPHEALAILEASNASNTHRLYSSERPHE
10   GLUASPILEHISHISTYRARGGLUGLNILE
11   LYSARGVALLYSASPSERGLUASPVALPRO
12   METVALLEUVALGLYASNLYSCYSASPLEU
13   PROSERARGTHRVALASPTHRLYSGLNALA
14   GLNASPLEUALAARGSERTYRGLYILEPRO
15   PHEILEGLUTHRSERALALYSTHRARGGLN
16   GLYVALASPASPALAPHETYRTHRLEUVAL
17   ARGGLUILEARGLYSHISLYSGLULYSMET
18   SERLYSASPGLYLYSLYSLYSLYSLYSLYS
19   SERLYSTHRLYSCYS

Entity 3, entity_3, 1 132 residues - 15266.923 Da.

1   ASNTHRILEARGVALPHELEUPROASNLYS
2   GLNARGTHRVALVALASNVALARGASNGLY
3   METSERLEUHISASPCYSLEUMETLYSALA
4   LEULYSVALARGGLYLEUGLNPROGLUCYS
5   CYSALAVALPHEARGLEULEUGLNGLUHIS
6   LYSGLYLYSLYSALAARGLEUASPTRPASN
7   THRASPALAALASERLEUILEGLYGLUGLU
8   LEUGLNVALASPPHELEUASPHISVALPRO
9   LEUTHRTHRHISASNPHEALAARGLYSTHR
10   PHELEULYSLEUALAPHECYSASPILECYS
11   GLNLYSPHELEULEUASNGLYPHEARGCYS
12   GLNTHRCYSGLYTYRLYSPHEHISGLUHIS
13   CYSSERTHRLYSVALPROTHRMETCYSVAL
14   ASPTRP

Entity 4, entity_4, 1 - C44 H85 N O8 P - 787.121 Da.

1   PCW

Entity 5, entity_5, 1 - C42 H78 N O10 P - 788.043 Da.

1   17F

Entity 6, entity_6, 1 - C10 H17 N6 O13 P3 - 522.196 Da.

1   GNP

Entity 7, entity_7, 1 - Mg - 24.305 Da.

1   MG

Entity 8, entity_8, 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: KRAS, [U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C], 0.2 mM; RBD-CRD, [U-12C, 14N, 1H], 0.2 mM; MSP, [U-12C, 14N, 1H], 0.4 mM

sample_2: KRAS, [U-12C, 14N, 1H], 0.2 mM; RBD-CRD, [U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C], 0.2 mM; MSP, [U-12C, 14N, 1H], 0.4 mM

sample_3: KRAS, [U-12C, 14N, 1H], 0.2 mM; RBD-CRD, [U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C], 0.2 mM

sample_4: KRAS, [U-12C, 14N, 1H], 0.2 mM; RBD-CRD, [U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C], 0.2 mM

sample_5: KRAS, [U-15N; Ile C-delta-13C, Met methyl-13C], 0.5 mM; RBD-CRD, [Leu C-delta-13C, Val C-gamma-13C], 0.5 mM

sample_6: RBD, [U-99% 15N; U-13C], 0.5 mM

sample_7: CRD, [U-99% 15N; U-13C], 0.3 mM

sample_conditions_1: ionic strength: 450 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 150 mM; pH: 5.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HMQCsample_1isotropicsample_conditions_1
2D 1H-13C HMQCsample_2isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1
2D 1H-13C HMQCsample_3isotropicsample_conditions_1
2D 1H-15N TROSYsample_3isotropicsample_conditions_1
2D 1H-13C HMQCsample_4isotropicsample_conditions_1
2D 1H-15N TROSYsample_4isotropicsample_conditions_1
3D 5N edited NOESYsample_5isotropicsample_conditions_2
3D HNCACBsample_6isotropicsample_conditions_1
3D CBCA(CO)NHsample_6isotropicsample_conditions_1
3D HNCAsample_6isotropicsample_conditions_1
3D HN(CO)CAsample_6isotropicsample_conditions_1
3D CBCA(CO)NHsample_7isotropicsample_conditions_1
3D HNCACBsample_7isotropicsample_conditions_1
3D HNCACOsample_6isotropicsample_conditions_1
3D HNCOsample_6isotropicsample_conditions_1
3D HNCACOsample_7isotropicsample_conditions_1
3D HNCOsample_7isotropicsample_conditions_1
3D HN(CO)CAsample_7isotropicsample_conditions_1
3D HNCAsample_7isotropicsample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

TopSpin, Bruker Biospin - collection

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

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

Sparky, Goddard - chemical shift assignment, data analysis, peak picking

HADDOCK, Bonvin - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 700 MHz

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