BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 27285

Title: Backbone 1H, 13C, and 15N Chemical Shift Assignments for VSV8 peptide bound to MHC H-2Kb (VSV8/Kb)   PubMed: 29101227

Deposition date: 2017-10-18 Original release date: 2017-12-14

Authors: Mallis, Robert; Arthanari, Haribabu; Lang, Matt; Reinherz, Ellis; Wagner, Gerhard

Citation: Mallis, Robert; Arthanari, Haribabu; Lang, Matt; Reinherz, Ellis; Wagner, Gerhard. "NMR-Directed Design of PreTCRbeta and pMHC Molecules Implies a Distinct Geometry for preTCR Relative to alphabetaTCR Recognition of pMHC"  J. Biol. Chem. 293, 754-766 (2018).

Assembly members:
H-2Kb, polymer, 281 residues, 32348.20 Da.
VSV8, polymer, 8 residues, Formula weight is not available
b2m, polymer, 99 residues, Formula weight is not available

Natural source:   Common Name: Mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pet11d

Entity Sequences (FASTA):
H-2Kb: MGPHSLRYFVTAVSRPGLGE PRYMEVGYVDDTEFVRFDSD AENPRYEPRARWMEQEGPEY WERETQKAKGNEQSFRVDLR TLLGYYNQSKGGSHTIQVIS GCEVGSDGRLLRGYQQYAYD GCDYIALNEDLKTWTAADMA ALITKHKWEQAGEAERLRAY LEGTCVEWLRRYLKNGNATL LRTDSPKAHVTHHSRPEDKV TLRCWALGFYPADITLTWQL NGEELIQDMELVETRPAGDG TFQKWASVVVPLGKEQYYTC HVYHQGLPEPLTLRWEPPPS T
VSV8: RGYVYQGL
b2m: IQKTPQIQVYSRHPPENGKP NILNCYVTQFHPPHIEIQML KNGKKIPKVEMSDMSFSKDW SFYILAHTEFTPTETDTYAC RVKHDSMAEPKTVYWDRDM

Data sets:
Data typeCount
13C chemical shifts296
15N chemical shifts196
1H chemical shifts196

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1H-2Kb1
2VSV82
3b2m3

Entities:

Entity 1, H-2Kb 281 residues - 32348.20 Da.

1   METGLYPROHISSERLEUARGTYRPHEVAL
2   THRALAVALSERARGPROGLYLEUGLYGLU
3   PROARGTYRMETGLUVALGLYTYRVALASP
4   ASPTHRGLUPHEVALARGPHEASPSERASP
5   ALAGLUASNPROARGTYRGLUPROARGALA
6   ARGTRPMETGLUGLNGLUGLYPROGLUTYR
7   TRPGLUARGGLUTHRGLNLYSALALYSGLY
8   ASNGLUGLNSERPHEARGVALASPLEUARG
9   THRLEULEUGLYTYRTYRASNGLNSERLYS
10   GLYGLYSERHISTHRILEGLNVALILESER
11   GLYCYSGLUVALGLYSERASPGLYARGLEU
12   LEUARGGLYTYRGLNGLNTYRALATYRASP
13   GLYCYSASPTYRILEALALEUASNGLUASP
14   LEULYSTHRTRPTHRALAALAASPMETALA
15   ALALEUILETHRLYSHISLYSTRPGLUGLN
16   ALAGLYGLUALAGLUARGLEUARGALATYR
17   LEUGLUGLYTHRCYSVALGLUTRPLEUARG
18   ARGTYRLEULYSASNGLYASNALATHRLEU
19   LEUARGTHRASPSERPROLYSALAHISVAL
20   THRHISHISSERARGPROGLUASPLYSVAL
21   THRLEUARGCYSTRPALALEUGLYPHETYR
22   PROALAASPILETHRLEUTHRTRPGLNLEU
23   ASNGLYGLUGLULEUILEGLNASPMETGLU
24   LEUVALGLUTHRARGPROALAGLYASPGLY
25   THRPHEGLNLYSTRPALASERVALVALVAL
26   PROLEUGLYLYSGLUGLNTYRTYRTHRCYS
27   HISVALTYRHISGLNGLYLEUPROGLUPRO
28   LEUTHRLEUARGTRPGLUPROPROPROSER
29   THR

Entity 2, VSV8 8 residues - Formula weight is not available

1   ARGGLYTYRVALTYRGLNGLYLEU

Entity 3, b2m 99 residues - Formula weight is not available

1   ILEGLNLYSTHRPROGLNILEGLNVALTYR
2   SERARGHISPROPROGLUASNGLYLYSPRO
3   ASNILELEUASNCYSTYRVALTHRGLNPHE
4   HISPROPROHISILEGLUILEGLNMETLEU
5   LYSASNGLYLYSLYSILEPROLYSVALGLU
6   METSERASPMETSERPHESERLYSASPTRP
7   SERPHETYRILELEUALAHISTHRGLUPHE
8   THRPROTHRGLUTHRASPTHRTYRALACYS
9   ARGVALLYSHISASPSERMETALAGLUPRO
10   LYSTHRVALTYRTRPASPARGASPMET

Samples:

sample_1: H-2Kb, [U-13C; U-15N; U-2H], 400 uM; VSV8 400 uM; sodium phosphate 50 mM; sodium chloride 150 mM; b2m 400 mM

sample_conditions_1: ionic strength: 470 mM; pH: 7.0; 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 HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCACOsample_1isotropicsample_conditions_1

Software:

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

TOPSPIN, Bruker Biospin - collection

Cara, Keller - chemical shift assignment, data analysis, peak picking

RASP, MacRaild - chemical shift assignment

SPARTA+, Shen and Bax - chemical shift calculation

NMR spectrometers:

  • Bruker UnityPlus 750 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance 500 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts