BMRB Entry 16738

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16738
MolProbity Validation Chart

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Title:
solution structure of human vaccinia related kinase1(VRK1)
Deposition date:
2010-02-19
Original release date:
2011-05-13
Authors:
Shin, Joon; Yoon, Ho Sup
Citation:

Citation: Shin, Joon; Chakraborty, Goutam; Bharatham, Nagakumar; Kang, Congbao; Tochio, Naoya; Koshiba, Seizo; Kigawa, Takanori; Kim, Wanil; Kim, Kyong-Tai; Yoon, Ho Sup. "NMR Solution Structure of Human Vaccinia-related Kinase 1 (VRK1) Reveals the C-terminal Tail Essential for Its Structural Stability and Autocatalytic Activity."  J. Biol. Chem. 286, 22131-22138 (2011).
PubMed: 21543316

Assembly members:

Assembly members:
VRK1, polymer, 360 residues, 41286.898 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   Vector: pET29b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VRK1: MPRVKAAQAGRQSSAKRHLA EQFAVGEIITDMAKKEWKVG LPIGQGGFGCIYLADMNSSE SVGSDAPCVVKVEPSDNGPL FTELKFYQRAAKPEQIQKWI RTRKLKYLGVPKYWGSGLHD KNGKSYRFMIMDRFGSDLQK IYEANAKRFSRKTVLQLSLR ILDILEYIHEHEYVHGDIKA SNLLLNYKNPDQVYLVDYGL AYRYCPEGVHKEYKEDPKRC HDGTIEFTSIDAHNGVAPSR RGDLEILGYCMIQWLTGHLP WEDNLKDPKYVRDSKIRYRE NIASLMDKCFPEKNKPGEIA KYMETVKLLDYTEKPLYENL RDILLQGLKAIGSKDDGKLD LSVVENGGLKAKTITKKRKK

Data sets:
Data typeCount
13C chemical shifts1170
15N chemical shifts337
1H chemical shifts2038

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1VRK11

Entities:

Entity 1, VRK1 360 residues - 41286.898 Da.

1   METPROARGVALLYSALAALAGLNALAGLY
2   ARGGLNSERSERALALYSARGHISLEUALA
3   GLUGLNPHEALAVALGLYGLUILEILETHR
4   ASPMETALALYSLYSGLUTRPLYSVALGLY
5   LEUPROILEGLYGLNGLYGLYPHEGLYCYS
6   ILETYRLEUALAASPMETASNSERSERGLU
7   SERVALGLYSERASPALAPROCYSVALVAL
8   LYSVALGLUPROSERASPASNGLYPROLEU
9   PHETHRGLULEULYSPHETYRGLNARGALA
10   ALALYSPROGLUGLNILEGLNLYSTRPILE
11   ARGTHRARGLYSLEULYSTYRLEUGLYVAL
12   PROLYSTYRTRPGLYSERGLYLEUHISASP
13   LYSASNGLYLYSSERTYRARGPHEMETILE
14   METASPARGPHEGLYSERASPLEUGLNLYS
15   ILETYRGLUALAASNALALYSARGPHESER
16   ARGLYSTHRVALLEUGLNLEUSERLEUARG
17   ILELEUASPILELEUGLUTYRILEHISGLU
18   HISGLUTYRVALHISGLYASPILELYSALA
19   SERASNLEULEULEUASNTYRLYSASNPRO
20   ASPGLNVALTYRLEUVALASPTYRGLYLEU
21   ALATYRARGTYRCYSPROGLUGLYVALHIS
22   LYSGLUTYRLYSGLUASPPROLYSARGCYS
23   HISASPGLYTHRILEGLUPHETHRSERILE
24   ASPALAHISASNGLYVALALAPROSERARG
25   ARGGLYASPLEUGLUILELEUGLYTYRCYS
26   METILEGLNTRPLEUTHRGLYHISLEUPRO
27   TRPGLUASPASNLEULYSASPPROLYSTYR
28   VALARGASPSERLYSILEARGTYRARGGLU
29   ASNILEALASERLEUMETASPLYSCYSPHE
30   PROGLULYSASNLYSPROGLYGLUILEALA
31   LYSTYRMETGLUTHRVALLYSLEULEUASP
32   TYRTHRGLULYSPROLEUTYRGLUASNLEU
33   ARGASPILELEULEUGLNGLYLEULYSALA
34   ILEGLYSERLYSASPASPGLYLYSLEUASP
35   LEUSERVALVALGLUASNGLYGLYLEULYS
36   ALALYSTHRILETHRLYSLYSARGLYSLYS

Samples:

sample_1: Vaccinia Related-Kinase 1, [U-100% 13C; U-100% 15N; U-80% 2H], 0.3 – 0.5 mM; Vaccinia Related-Kinase 1, [U-100% 15N; U-50% 2H], 0.3 – 0.5 mM; Vaccinia Related-Kinase 1, [U-100% 15N], 0.1 – 0.2 mM; H2O 90%; D2O 10%

sample_2: Vaccinia Related-Kinase 1, [U-100% 13C; U-100% 15N; U-70% 2H], 0.3 – 0.5 mM; Vaccinia Related-Kinase 1, [13C;15N]-Val,Ile,Leu; [U-100% 2H], 0.3 – 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - generation of initial structures

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 11506 16715
PDB
DBJ BAA19108 BAF82799 BAI47070
GB AAI03762 AAI12076 AAI13511 AAQ02593 AIC55301
REF NP_001244605 NP_003375 XP_003902302 XP_003928890 XP_004055717
SP Q99986
AlphaFold Q99986

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