BMRB Entry 25116

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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/BMR25116
MolProbity Validation Chart

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Title:
NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc
Deposition date:
2014-07-29
Original release date:
2015-05-27
Authors:
Mazhab-Jafari, Mohammad T.; Stathopoulos, Peter B.; Marshall, Christopher B.; Ikura, Mitsuhiko
Citation:

Citation: Mazhab-Jafari, Mohammad T.; Marshall, Christopher B.; Smith, Matthew J.; Gasmi-Seabrook, Genevieve M. C.; Stathopoulos, Peter B.; Inagaki, Fuyuhiko; Kay, Lewis E.; Neel, Benjamin G.; Ikura, Mitsuhiko. "Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site"  Proc. Natl. Acad. Sci. U. S. A. 112, 6625-6630 (2015).
PubMed: 25941399

Assembly members:

Assembly members:
K-Ras, polymer, 187 residues, 8696.952 Da.
membrane_scaffold_protein, polymer, 200 residues, 63628.461 Da.
A-RafRBD, polymer, 73 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
K-Ras: GSMTEYKLVVVGAGGVGKSA LTIQLIQNHFVDEYDPTIED SYRKQVVIDGETCLLDILDT AGQEEYSAMRDQYMRTGEGF LCVFAINNTKSFEDIHHYRE QIKRVKDSEDVPMVLVGNKC DLPSRTVDTKQAQDLARSYG IPFIETSAKTRQGVDDAFYT LVREIRKHKEKMSKDGKKKK KKSKTKC
membrane_scaffold_protein: GPLKLLDNWDSVTSTFSKLR EQLGPVTQEFWDNLEKETEG LRQEMSKDLEEVKAKVQPYL DDFQKKWQEEMELYRQKVEP LRAELQEGARQKLHELQEKL SPLGEEMRDRARAHVDALRT HLAPYSDELRQRLAARLEAL KENGGARLAEYHAKATEHLS TLSEKAKPALEDLRGELLPV LESFKVSFLSALEEYTKKLN
A-RafRBD: GTVKVYLPNKQRTVVTVRDG MSVYDSLDKALKVRGLNQDC CVVYRLIKGRKTVTAWDTAI APLDGEELIVEVL

Data sets:
Data typeCount
13C chemical shifts13
1H chemical shifts39

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1K-Ras1
2membrane scaffold protein2
3A-RafRBD3

Entities:

Entity 1, K-Ras 187 residues - 8696.952 Da.

1   GLYSERMETTHRGLUTYRLYSLEUVALVAL
2   VALGLYALAGLYGLYVALGLYLYSSERALA
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 2, membrane scaffold protein 200 residues - 63628.461 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   GLUASPLEUARGGLYGLULEULEUPROVAL
19   LEUGLUSERPHELYSVALSERPHELEUSER
20   ALALEUGLUGLUTYRTHRLYSLYSLEUASN

Entity 3, A-RafRBD 73 residues - Formula weight is not available

1   GLYTHRVALLYSVALTYRLEUPROASNLYS
2   GLNARGTHRVALVALTHRVALARGASPGLY
3   METSERVALTYRASPSERLEUASPLYSALA
4   LEULYSVALARGGLYLEUASNGLNASPCYS
5   CYSVALVALTYRARGLEUILELYSGLYARG
6   LYSTHRVALTHRALATRPASPTHRALAILE
7   ALAPROLEUASPGLYGLUGLULEUILEVAL
8   GLUVALLEU

Samples:

sample_1: K-Ras, U-15N, Ile C-delta-13C, 0.6 mM; membrane scaffold protein 0.6 mM; A-RafRBD 0.7 mM; sodium chloride 100 mM; Magnesium 5 mM; TRIS 20 mM; TCEP 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 0.6 mM; 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM; 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM; 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM

sample_2: K-Ras 0.7 mM; membrane scaffold protein 0.7 mM; A-RafRBD, U-15N, Ile C-delta-13C, 0.6 mM; Magnesium 5 mM; TRIS 20 mM; sodium chloride 100 mM; TCEP 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 0.7 mM; 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM; 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM; 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM

sample_3: K-Ras, U-15N, Ile C-delta-13C, 0.6 mM; A-RafRBD 0.7 mM; membrane scaffold protein 0.6 mM; TRIS 20 mM; sodium chloride 100 mM; Magnesium 5 mM; TCEP 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 0.6 mM; 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM; 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM; 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM; 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt) 0.65 mM

sample_4: K-Ras 0.7 mM; A-RafRBD, U-15N, Ile C-delta-13C, 0.6 mM; membrane scaffold protein 0.7 mM; TRIS 20 mM; sodium chloride 100 mM; Magnesium 5 mM; TCEP 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 0.7 mM; 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM; 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM; 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM; 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt) 0.65 mM

sample_conditions_1: ionic strength: 0.105 M; pH: 7.4; pressure: 1 atm; temperature: 298.2 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HMQCsample_1isotropicsample_conditions_1
2D 1H-13C HMQCsample_2isotropicsample_conditions_1
2D 1H-13C HMQCsample_3isotropicsample_conditions_1
2D 1H-13C HMQCsample_4isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

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

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

SPARKY, Goddard - data analysis

TOPSPIN, Bruker Biospin - collection

CHARMM-GUI, CHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im) - structure solution

HADDOCK, Alexandre Bonvin - structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

BMRB 17785 18529 25114 25115 26635
PDB
DBJ BAE33023 BAE37609 BAF85199 BAJ17756
EMBL CAA25624 CAA26295 CAA37336 CAA59755 CAA76678
GB AAA35689 AAA35690 AAA36554 AAA42011 AAA49429
PIR A54321
PRF 0909262B
REF NP_001003744 NP_001028153 NP_001095209 NP_001103471 NP_001184192
SP O42277 P79800 Q05147 Q07983 Q5EFX7
TPG DAA29418
AlphaFold O42277 P79800 Q05147 Q07983 Q5EFX7 A0A024RAV5 Q9UCT8