BMRBj - BMREntryMaster

Found 1 Document (2.293 seconds)

BMRB: 30639

1AV1

NMR data-driven model of KRas-GMPPNP:RBD-CRD complex tethered to a nanodisc (state A)

Authors

Fang, Z., Lee, K., Gasmi-Seabrook, G., Ikura, M., Marshall, C.B.

Assembly

Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase

Entity

1. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 1 (polymer), 198 monomers, 23042.79 × 2 Da Detail

LKLLDNWDSV TSTFSKLREQ LGPVTQEFWD NLEKETEGLR QEMSKDLEEV KAKVQPYLDD FQKKWQEEME LYRQKVEPLR AELQEGARQK LHELQEKLSP LGEEMRDRAR AHVDALRTHL APYSDELRQR LAARLEALKE NGGARLAEYH AKATEHLSTL SEKAKPALED LRQGLLPVLE SFKVSFLSAL EEYTKKLN

2. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 2 (polymer), 185 monomers, 21080.80 Da Detail

MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPTIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ YMRTGEGFLC VFAINNTKSF EDIHHYREQI KRVKDSEDVP MVLVGNKCDL PSRTVDTKQA QDLARSYGIP FIETSAKTRQ GVDDAFYTLV REIRKHKEKM SKDGKKKKKK SKTKC

3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3 (polymer), 132 monomers, 15241.71 Da Detail

NTIRVFLPNK QRTVVNVRNG MSLHDCLMKA LKVRGLQPEC CAVFRLLQEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DW

4. 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE (non-polymer), 787.121 × 64 Da
5. O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine (non-polymer), 788.043 × 15 Da
6. PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (non-polymer), 522.196 Da
7. MAGNESIUM ION (non-polymer), 24.305 Da
8. ZINC ION (non-polymer), 65.409 × 2 Da

Total weight

145281.8 Da

Max. entity weight

23042.79 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 42.1 %, Completeness: 11.1 %, Completeness (bb): 16.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	11.1 % (688 of 6176)	11.0 % (356 of 3241)	5.1 % (122 of 2388)	38.4 % (210 of 547)
Backbone	16.6 % (508 of 3060)	22.3 % (232 of 1040)	4.3 % (66 of 1520)	42.0 % (210 of 500)
Sidechain	5.7 % (205 of 3606)	5.7 % (125 of 2201)	5.9 % (80 of 1358)	0.0 % (0 of 47)
Aromatic	0.9 % (4 of 432)	1.9 % (4 of 216)	0.0 % (0 of 211)	0.0 % (0 of 5)
Methyl	18.4 % (102 of 554)	18.4 % (51 of 277)	18.4 % (51 of 277)

1. entity 1

2. entity 2

3. entity 3

NTIRVFLPNK QRTVVNVRNG MSLHDCLMKA LKVRGLQPEC CAVFRLLQEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C KRAS, 0.2 mM U-12C, 14N, 1H RBD-CRD, 0.4 mM U-12C, 14N, 1H MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KRAS	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]	0.2 mM
2	RBD-CRD	[U-12C, 14N, 1H]	0.2 mM
3	MSP	[U-12C, 14N, 1H]	0.4 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM U-12C, 14N, 1H KRAS, 0.2 mM U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C RBD-CRD, 0.4 mM U-12C, 14N, 1H MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C, 14N, 1H]	0.2 mM
5	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]	0.2 mM
6	MSP	[U-12C, 14N, 1H]	0.4 mM

Sample #3

#	Name	Isotope labeling	Type	Concentration
7	KRAS	[U-12C, 14N, 1H]		0.2 mM
8	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

Sample #4

#	Name	Isotope labeling	Type	Concentration
9	KRAS	[U-12C, 14N, 1H]		0.2 mM
10	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM U-15N; Ile C-delta-13C, Met methyl-13C KRAS, 0.5 mM Leu C-delta-13C, Val C-gamma-13C, RBD-CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	KRAS	[U-15N; Ile C-delta-13C, Met methyl-13C]		0.5 mM
12	RBD-CRD	[Leu C-delta-13C, Val C-gamma-13C]		0.5 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 6PTS, Strand ID: A, B, C, D Detail

Release date

2019-08-15

Citation

Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane
Fang, Z., Lee, K.Y., Huo, K.G., Gasmi-Seabrook, G., Zheng, L., Moghal, N., Tsao, M.S., Ikura, M., Marshall, C.B.
Proc. Natl. Acad. Sci. U. S. A. (2020), 117, 12101-12108, PubMed 32414921 , DOI 10.1073/pnas.1914076117 , Abstract

Related entities 1. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 1, : 1 : 15 : 3 : 30 entities Detail

Related entities 2. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 2, : 100 entities Detail

Related entities 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 6 : 14 : 38 entities Detail

Interaction partners 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 19 interactors Detail

More details for 19 interactors identified by 12 citations

Experiments performed 20 experiments Detail

1 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C KRAS, 0.2 mM U-12C, 14N, 1H RBD-CRD, 0.4 mM U-12C, 14N, 1H MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KRAS	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]	0.2 mM
2	RBD-CRD	[U-12C, 14N, 1H]	0.2 mM
3	MSP	[U-12C, 14N, 1H]	0.4 mM

2 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.2 mM U-12C, 14N, 1H KRAS, 0.2 mM U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C RBD-CRD, 0.4 mM U-12C, 14N, 1H MSP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C, 14N, 1H]	0.2 mM
5	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]	0.2 mM
6	MSP	[U-12C, 14N, 1H]	0.4 mM

3 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	KRAS	[U-12C, 14N, 1H]	0.2 mM
5	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]	0.2 mM
6	MSP	[U-12C, 14N, 1H]	0.4 mM

4 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	KRAS	[U-12C, 14N, 1H]		0.2 mM
8	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

5 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	KRAS	[U-12C, 14N, 1H]		0.2 mM
8	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

6 2D 1H-13C HMQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	KRAS	[U-12C, 14N, 1H]		0.2 mM
10	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

7 2D 1H-15N TROSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
9	KRAS	[U-12C, 14N, 1H]		0.2 mM
10	RBD-CRD	[U-2H; U-15N; Ile Leu C-delta-13C, Val C-gamma-13C]		0.2 mM

8 3D 5N edited NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 0.5 mM U-15N; Ile C-delta-13C, Met methyl-13C KRAS, 0.5 mM Leu C-delta-13C, Val C-gamma-13C, RBD-CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
11	KRAS	[U-15N; Ile C-delta-13C, Met methyl-13C]		0.5 mM
12	RBD-CRD	[Leu C-delta-13C, Val C-gamma-13C]		0.5 mM

9 3D HNCACB

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

10 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

11 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

12 3D HN(CO)CA

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

13 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

14 3D HNCACB

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

15 3D HNCACO

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

16 3D HNCO

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.5 mM [U-99% 15N]; [U-13C]; RBD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
13	RBD	[U-99% 15N; U-13C]		0.5 mM

17 3D HNCACO

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

18 3D HNCO

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

19 3D HN(CO)CA

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

20 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.3 mM [U-99% 15N]; [U-13C]; CRD, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
14	CRD	[U-99% 15N; U-13C]		0.3 mM

Chemical shift validation 10 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30639_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30639_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	557		55.1 (chain: 2, length: 185), 78.0 (chain: 3, length: 132)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 185, Sequence coverage: 55.1%
  - Entity_assembly_ID: 3, Chain length: 132, Sequence coverage: 78.0%
- Total number of assignments
  - ¹H chemical shifts: 318
  - ¹⁵N chemical shifts: 198
  - ¹³C chemical shifts: 41
- Completeness of assignments
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 3
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2
  - Chain_ID: 3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1143	121	10.6
¹⁵N chemical shifts	204	97	47.5
¹³C chemical shifts	845	24	2.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	378	97	25.7
¹⁵N chemical shifts	181	97	53.6
¹³C chemical shifts	370	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	765	24	3.1
¹⁵N chemical shifts	23	0	0.0
¹³C chemical shifts	475	24	5.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	24	23.8
¹³C chemical shifts	101	24	23.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	0	0.0
¹³C chemical shifts	70	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	830	117	14.1
¹⁵N chemical shifts	151	101	66.9
¹³C chemical shifts	621	17	2.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	266	101	38.0
¹⁵N chemical shifts	128	101	78.9
¹³C chemical shifts	264	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	564	16	2.8
¹⁵N chemical shifts	23	0	0.0
¹³C chemical shifts	357	17	4.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	16	20.8
¹³C chemical shifts	77	17	22.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	0	0.0
¹⁵N chemical shifts	2	0	0.0
¹³C chemical shifts	71	0	0.0

Keywords RAS-RAF-nanodisc complex, SIGNALING PROTEIN, protein-protein-bilayer complex, small GTPase

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Found 1 Document (2.293 seconds)

BMRB: 30639

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Sample #7

Related entities 1. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 1, : 1 : 15 : 3 : 30 entities Detail

Related entities 2. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 2, : 100 entities Detail

Related entities 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 6 : 14 : 38 entities Detail

Interaction partners 3. Apolipoprotein A-I, GTPase KRas, RAF proto-oncogene serine/threonine-protein kinase, entity 3, : 19 interactors Detail

Experiments performed 20 experiments Detail

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Chemical shift validation 10 contents Detail