BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 18461

Title: Chemical shift assignments and backbone dynamics of H-Ras-GppNHp bound to Ras-binding domain of cRaf1.   PubMed: 21930707

Authors: Araki, Mitsugu; Tamura, Atsuo

Citation: Araki, Mitsugu; Shima, Fumi; Yoshikawa, Yoko; Muraoka, Shin; Ijiri, Yuichi; Nagahara, Yuka; Shirono, Tomoya; Kataoka, Tohru; Tamura, Atsuo. "Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers"  J. Biol. Chem. 286, 39644-39653 (2011).

Assembly members:
entity_1, polymer, 172 residues, 18861.303 Da.
entity_GNP, non-polymer, 522.196 Da.
entity_MG, non-polymer, 24.305 Da.
entity_HOH, water, 18.015 Da.
entry_2, polymer, . residues, Formula weight is not available

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GPLGSDMTEYKLVVVGAGGV GKSALTIQLIQNHFVDEYDP TIEDSYRKQVVIDGETCLLD ILDTAGQEEYSAMRDQYMRT GEGFLCVFAINNTKSFEDIH QYREQIKRVKDSDDVPMVLV GNKCDLAARTVESRQAQDLA RSYGIPYIETSAKTRQGVED AFYTLVREIRQH
entry_2: XXXSNTIRVFLPNKQRTVVN VRNGMSLHDCLMKALKVRGL QPECCAVFRLLHEHKGKKAR LDWNTDAASLIGEELQVDF

Data sets:
Data typeCount
1H chemical shifts162
13C chemical shifts163
15N chemical shifts162
heteronuclear NOE values134
T1 relaxation values134
T2 relaxation values135

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1H-Ras-GppNHp1
2PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER2
3MAGNESIUM ION3
4water4
5Ras-binding domain of cRaf15

Entities:

Entity 1, H-Ras-GppNHp 172 residues - 18861.303 Da.

1   GLYPROLEUGLYSERASPMETTHRGLUTYR
2   LYSLEUVALVALVALGLYALAGLYGLYVAL
3   GLYLYSSERALALEUTHRILEGLNLEUILE
4   GLNASNHISPHEVALASPGLUTYRASPPRO
5   THRILEGLUASPSERTYRARGLYSGLNVAL
6   VALILEASPGLYGLUTHRCYSLEULEUASP
7   ILELEUASPTHRALAGLYGLNGLUGLUTYR
8   SERALAMETARGASPGLNTYRMETARGTHR
9   GLYGLUGLYPHELEUCYSVALPHEALAILE
10   ASNASNTHRLYSSERPHEGLUASPILEHIS
11   GLNTYRARGGLUGLNILELYSARGVALLYS
12   ASPSERASPASPVALPROMETVALLEUVAL
13   GLYASNLYSCYSASPLEUALAALAARGTHR
14   VALGLUSERARGGLNALAGLNASPLEUALA
15   ARGSERTYRGLYILEPROTYRILEGLUTHR
16   SERALALYSTHRARGGLNGLYVALGLUASP
17   ALAPHETYRTHRLEUVALARGGLUILEARG
18   GLNHIS

Entity 2, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER - C10 H17 N6 O13 P3 - 522.196 Da.

1   GNP

Entity 3, MAGNESIUM ION - Mg - 24.305 Da.

1   MG

Entity 4, water - 18.015 Da.

1   HOH

Entity 5, Ras-binding domain of cRaf1 - Formula weight is not available

1   XXXSERASNTHRILEARGVALPHE
2   LEUPROASNLYSGLNARGTHRVALVALASN
3   VALARGASNGLYMETSERLEUHISASPCYS
4   LEUMETLYSALALEULYSVALARGGLYLEU
5   GLNPROGLUCYSCYSALAVALPHEARGLEU
6   LEUHISGLUHISLYSGLYLYSLYSALAARG
7   LEUASPTRPASNTHRASPALAALASERLEU
8   ILEGLYGLUGLULEUGLNVALASPPHE

Samples:

sample_1: H-Ras-GppNHp, [U-98% 13C; U-98% 15N], 1-2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 1-2 mM; MAGNESIUM ION 10 mM; sodium chloride 150 mM; sodium phosphate 25 mM; Ras-binding domain of cRaf1 1-2 mM

sample_2: H-Ras-GppNHp, [U-98% 15N], 1-2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 1-2 mM; MAGNESIUM ION 10 mM; sodium chloride 150 mM; sodium phosphate 25 mM; Ras-binding domain of cRaf1 1-2 mM

sample_conditions_1: temperature: 298 K; pH: 6.8; pressure: 1 atm; ionic strength: 0.24 M

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - peak picking

NMR spectrometers:

  • Bruker DMX 750 MHz

Related Database Links:

BMRB 10051 17183 17610 17678 18479 18629 25730
PDB
DBJ BAB61869 BAB61870 BAB88314 BAB88315 BAB88316 BAB39743 BAB39748 BAB83675 BAE24820 BAG10817
EMBL CAA25322 CAA25624 CAA27258 CAA35240 CAA90306 CAA27204 CAH92939
GB AAA36554 AAA42009 AAA46568 AAA46569 AAA46570 AAA42001 AAB27591 AAH15273 AAH18119 AAH62071
PIR A43816 TVMVNS
PRF 0904302A 1604384A
REF NP_001017003 NP_001018465 NP_001084278 NP_001091711 NP_001123913 NP_001095975 NP_001126730 NP_001253231 NP_002871 NP_036771
SP P01112 P01113 P01114 P01115 P08642 A7E3S4 P04049 P11345 Q5R5M7 Q99N57
TPG DAA13500 DAA16778 DAA16781 DAA16798