Solution structure of human full-length vaccinia related kinase 1 (VRK1)
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
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
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 VQKSolvent 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 % |
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 % |
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 % |
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 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Bruker Avance - 900 MHz
State isotropic, 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 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_11506_2rsv.nef |
Input source #2: Coordindates | 2rsv.cif |
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
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
---------------10--------20--------30--------40--------50--------60--------70--------80--------90--- GSSGSSGMPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKP |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSSGSSGMPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKP --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ----100-------110-------120-------130-------140-------150-------160-------170-------180-------190--- EQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQV |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| EQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQV -------110-------120-------130-------140-------150-------160-------170-------180-------190-------200 ----200-------210-------220-------230-------240-------250-------260-------270-------280-------290--- YLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| YLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEK -------210-------220-------230-------240-------250-------260-------270-------280-------290-------300 ----300-------310-------320-------330-------340-------350-------360-------370-------380-------390--- NKPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRKKEIEESKEPGVEDTEWSNTQTEEAIQTRSRTRKR |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NKPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRKKEIEESKEPGVEDTEWSNTQTEEAIQTRSRTRKR -------310-------320-------330-------340-------350-------360-------370-------380-------390-------400 --- VQK ||| VQK ---
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 403 | 0 | 0 | 100.0 |
Content subtype: combined_11506_2rsv.nef
Assigned chemical shifts
---------------10--------20--------30--------40--------50--------60--------70--------80--------90--- GSSGSSGMPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKP |||||||||| ||| ||||||||||||||||||||||||||||||||||||||| |||||||||||||||| ||||||||||||||||| ..SGSSGMPRVK.....RQS.....LAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMN..ESVGSDAPCVVKVEPS.NGPLFTELKFYQRAAKP ----100-------110-------120-------130-------140-------150-------160-------170-------180-------190--- EQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQV |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| EQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQV ----200-------210-------220-------230-------240-------250-------260-------270-------280-------290--- YLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEK |||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| YLVDYGLAYRYCPEGV..EYKEDPKRCHDGTIEFTSIDAHNGVA..RRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEK ----300-------310-------320-------330-------340-------350-------360-------370-------380-------390--- NKPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRKKEIEESKEPGVEDTEWSNTQTEEAIQTRSRTRKR ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||| |||||||||||||||||| | | NKPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVEN.GLK..TITK.RKKEIEESKEPGVEDTEW......E..........R --- VQK ||| VQK
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 2539 | 599 | 23.6 |
13C chemical shifts | 1857 | 1305 | 70.3 |
15N chemical shifts | 445 | 349 | 78.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 821 | 343 | 41.8 |
13C chemical shifts | 806 | 726 | 90.1 |
15N chemical shifts | 386 | 343 | 88.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 1718 | 256 | 14.9 |
13C chemical shifts | 1051 | 579 | 55.1 |
15N chemical shifts | 59 | 6 | 10.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 204 | 174 | 85.3 |
13C chemical shifts | 204 | 175 | 85.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 179 | 70 | 39.1 |
13C chemical shifts | 173 | 64 | 37.0 |
15N chemical shifts | 6 | 6 | 100.0 |
Distance restraints
---------------10--------20--------30--------40--------50--------60--------70--------80--------90--- GSSGSSGMPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKP |||||||||||||||||||||| || |||||||||| || || |||||| | || ||||||||||||| ..........................AEQFAVGEIITDMAKKEWKVGL.IG...FGCIYLADMN....VG.DA.CVVKVE.S.NG.LFTELKFYQRAAK. ---------------10--------20--------30--------40--------50--------60--------70--------80--------90--- ----100-------110-------120-------130-------140-------150-------160-------170-------180-------190--- EQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQV ||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| EQIQKWIRTRKLKYLGV.KYWGSGLHDK.GKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKN.DQV ----100-------110-------120-------130-------140-------150-------160-------170-------180-------190--- ----200-------210-------220-------230-------240-------250-------260-------270-------280-------290--- YLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEK |||||||||||| ||| |||| |||||||||||||||||||| ||||||||||||||||||| ||||||| |||||||||||||||||||||| || YLVDYGLAYRYC.EGV...YKED.KRCHDGTIEFTSIDAHNGVA...RGDLEILGYCMIQWLTGHL.WEDNLKD.KYVRDSKIRYRENIASLMDKCF.EK ----200-------210-------220-------230-------240-------250-------260-------270-------280-------290--- ----300-------310-------320-------330-------340-------350-------360-------370-------380-------390--- NKPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRKKEIEESKEPGVEDTEWSNTQTEEAIQTRSRTRKR | |||||||||||||||||| |||||||||||||||||||||||||||||| N..GEIAKYMETVKLLDYTEK.LYENLRDILLQGLKAIGSKDDGKLDLSVVE ----300-------310-------320-------330-------340----- --- VQK
Dihedral angle restraints
RDC restraints