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BMRB: 11506

2RSV

Solution structure of human full-length vaccinia related kinase 1 (VRK1)

Authors

Koshiba, S., Tochio, N., Yokoyama, J., Kigawa, T.

Assembly

human full-length vaccinia related kinase 1 (VRK1)

Entity

1. human full-length vaccinia related kinase 1 (VRK1) (polymer, Thiol state: all free), 403 monomers, 45994.94 Da Detail

GSSGSSGMPR VKAAQAGRQS SAKRHLAEQF AVGEIITDMA KKEWKVGLPI GQGGFGCIYL ADMNSSESVG SDAPCVVKVE PSDNGPLFTE LKFYQRAAKP EQIQKWIRTR KLKYLGVPKY WGSGLHDKNG KSYRFMIMDR FGSDLQKIYE ANAKRFSRKT VLQLSLRILD ILEYIHEHEY VHGDIKASNL LLNYKNPDQV YLVDYGLAYR YCPEGVHKEY KEDPKRCHDG TIEFTSIDAH NGVAPSRRGD LEILGYCMIQ WLTGHLPWED NLKDPKYVRD SKIRYRENIA SLMDKCFPEK NKPGEIAKYM ETVKLLDYTE KPLYENLRDI LLQGLKAIGS KDDGKLDLSV VENGGLKAKT ITKKRKKEIE ESKEPGVEDT EWSNTQTEEA IQTRSRTRKR VQK

Formula weight

45994.94 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 58.4 %, Completeness (bb): 80.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	58.4 % (2814 of 4817)	40.8 % (1036 of 2539)	75.8 % (1408 of 1857)	87.9 % (370 of 421)
Backbone	80.0 % (1907 of 2384)	57.0 % (468 of 821)	91.6 % (1078 of 1177)	93.5 % (361 of 386)
Sidechain	44.0 % (1234 of 2804)	32.9 % (565 of 1718)	62.8 % (660 of 1051)	25.7 % (9 of 35)
Aromatic	50.6 % (181 of 358)	53.6 % (96 of 179)	45.7 % (79 of 173)	100.0 % (6 of 6)
Methyl	89.8 % (352 of 392)	90.3 % (177 of 196)	89.3 % (175 of 196)

1. entity

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1	protein	0.4 mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		100 mM
4	glutamic acid	natural abundance		50 mM
5	arginine	natural abundance		50 mM
6	DTT	[U-2H]		1 mM
7	sodium azide	natural abundance		0.02 %
8	H2O		solvent	90 %
9	D2O		solvent	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
10	entity	[U-13C; U-15N; U-2H; 1H ILE, LEU, VAL METHYL; 1H PHE, TYR EPSILON] VRK1	protein	0.4 mM
11	TRIS	[U-2H]		20 mM
12	sodium chloride	natural abundance		100 mM
13	glutamic acid	natural abundance		50 mM
14	arginine	natural abundance		50 mM
15	DTT	[U-2H]		1 mM
16	sodium azide	natural abundance		0.02 %
17	H2O		solvent	90 %
18	D2O		solvent	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
19	entity	[U-15N; U-2H; 13C,1H ILE, LEU, VAL METHYL; 13C,1H PHE DELTA/EPSILON/ZETA] VRK1	protein	0.4 mM
20	TRIS	[U-2H]		20 mM
21	sodium chloride	natural abundance		100 mM
22	glutamic acid	natural abundance		50 mM
23	arginine	natural abundance		50 mM
24	DTT	[U-2H]		1 mM
25	sodium azide	natural abundance		0.02 %
26	H2O		solvent	90 %
27	D2O		solvent	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
28	entity	SAIL-VRK1	protein	0.4 mM
29	TRIS	[U-2H]		20 mM
30	sodium chloride	natural abundance		100 mM
31	glutamic acid	natural abundance		50 mM
32	arginine	natural abundance		50 mM
33	DTT	[U-2H]		1 mM
34	sodium azide	natural abundance		0.02 %
35	H2O		solvent	90 %
36	D2O		solvent	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.64 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.64 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.33 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 18 models in PDB: 2RSV, Strand ID: A Detail

Release date

2013-12-01

Citation

A strategy for structure determination of large molecular weight protein using isotope labeling methodology with cell-free protein systhesis: application to 45 kDa human vaccinia related kianse 1 (VRK1)
Koshiba, S., Tochio, N., Yokoyama, J., Yoon, H., Kigawa, T.
Not known

Related entities 1. human full-length vaccinia related kinase 1 (VRK1), : 1 : 23 : 53 entities Detail

Interaction partners 1. human full-length vaccinia related kinase 1 (VRK1), : 22 interactors Detail

More details for 22 interactors identified by 16 citations

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY