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 27249

Title: Backbone amide and AILV methyl chemical shift assignments for H2-Dd, a murine class I major histocompatibility molecule heavy chain   PubMed: 29988068

Deposition date: 2017-09-08 Original release date: 2018-08-16

Authors: Sgourakis, Nikolaos; McShan, Andrew; Natarajan, Kannan; Kumirov, Vlad; Margulies, David; Nerli, Santrupti; Badstuebner, Mareike

Citation: McShan, Andrew; Natarajan, Kannan; Kumirov, Vlad; Flores-Solis, David; Jiang, Jiansheng; Badstubner, Mareike; Toor, Jugmohit; Bagshaw, Clive; Kovrigin, Evgenii; Margulies, David; Sgourakis, Nikolaos. "Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle"  Nat. Chem. Biol. 14, 811-820 (2018).

Assembly members:
H2-Dd, polymer, 277 residues, Formula weight is not available
Beta-2_microglobulin, polymer, 100 residues, Formula weight is not available
P18-I10, polymer, 10 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: pET-3a

Entity Sequences (FASTA):
H2-Dd: MSHSLRYFVTAVSRPGFGEP RYMEVGYVDNTEFVRFDSDA ENPRYEPRARWIEQEGPEYW ERETRRAKGNEQSFRVDLRT ALRYYNQSAGGSHTLQWMAG CDVESDGRLLRGYWQFAYDG CDYIALNEDLKTWTAADMAA QITRRKWEQAGAAERDRAYL EGECVEWLRRYLKNGNATLL RTDPPKAHVTHHRRPEGDVT LRCWALGFYPADITLTWQLN GEELTQEMELVETRPAGDGT FQKWASVVVPLGKEQKYTCH VEHEGLPEPLTLRWGKE
Beta-2_microglobulin: MIQRTPKIQVYSRHPAENGK SNFLNCYVSGFHPSDIEVDL LKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYA CRVNHVTLSQPKIVKWDRDM
P18-I10: RGPGRAFVTI

Data sets:
Data typeCount
13C chemical shifts801
15N chemical shifts233
1H chemical shifts530

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Antigen Peptide3
2Heavy Chain1
3Light Chain2

Entities:

Entity 3, Antigen Peptide 10 residues - Formula weight is not available

1   ARGGLYPROGLYARGALAPHEVALTHRILE

Entity 1, Heavy Chain 277 residues - Formula weight is not available

1   METSERHISSERLEUARGTYRPHEVALTHR
2   ALAVALSERARGPROGLYPHEGLYGLUPRO
3   ARGTYRMETGLUVALGLYTYRVALASPASN
4   THRGLUPHEVALARGPHEASPSERASPALA
5   GLUASNPROARGTYRGLUPROARGALAARG
6   TRPILEGLUGLNGLUGLYPROGLUTYRTRP
7   GLUARGGLUTHRARGARGALALYSGLYASN
8   GLUGLNSERPHEARGVALASPLEUARGTHR
9   ALALEUARGTYRTYRASNGLNSERALAGLY
10   GLYSERHISTHRLEUGLNTRPMETALAGLY
11   CYSASPVALGLUSERASPGLYARGLEULEU
12   ARGGLYTYRTRPGLNPHEALATYRASPGLY
13   CYSASPTYRILEALALEUASNGLUASPLEU
14   LYSTHRTRPTHRALAALAASPMETALAALA
15   GLNILETHRARGARGLYSTRPGLUGLNALA
16   GLYALAALAGLUARGASPARGALATYRLEU
17   GLUGLYGLUCYSVALGLUTRPLEUARGARG
18   TYRLEULYSASNGLYASNALATHRLEULEU
19   ARGTHRASPPROPROLYSALAHISVALTHR
20   HISHISARGARGPROGLUGLYASPVALTHR
21   LEUARGCYSTRPALALEUGLYPHETYRPRO
22   ALAASPILETHRLEUTHRTRPGLNLEUASN
23   GLYGLUGLULEUTHRGLNGLUMETGLULEU
24   VALGLUTHRARGPROALAGLYASPGLYTHR
25   PHEGLNLYSTRPALASERVALVALVALPRO
26   LEUGLYLYSGLUGLNLYSTYRTHRCYSHIS
27   VALGLUHISGLUGLYLEUPROGLUPROLEU
28   THRLEUARGTRPGLYLYSGLU

Entity 2, Light Chain 100 residues - Formula weight is not available

1   METILEGLNARGTHRPROLYSILEGLNVAL
2   TYRSERARGHISPROALAGLUASNGLYLYS
3   SERASNPHELEUASNCYSTYRVALSERGLY
4   PHEHISPROSERASPILEGLUVALASPLEU
5   LEULYSASNGLYGLUARGILEGLULYSVAL
6   GLUHISSERASPLEUSERPHESERLYSASP
7   TRPSERPHETYRLEULEUTYRTYRTHRGLU
8   PHETHRPROTHRGLULYSASPGLUTYRALA
9   CYSARGVALASNHISVALTHRLEUSERGLN
10   PROLYSILEVALLYSTRPASPARGASPMET

Samples:

triple_labeled_pMHC-I: H2-Dd, [U-13C; U-15N; U-2H], 1 mM; Beta-2 microglobulin 1 mM; P18-I10 1 mM

AILV_methyl_pMHC-I: H2-Dd, [U-15N; U-2H; U-13C; AILV], 1 mM; P18-I10 1 mM; Beta-2 microglobulin 1 mM

ILV*_pMHC-I: H2-Dd, [U-15N; U-2H; U-13C-all methyl carbons], 1 mM; P18-I10 1 mM; Beta-2 microglobulin 1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQCtriple_labeled_pMHC-Iisotropicsample_conditions_1
3D HNCAtriple_labeled_pMHC-Iisotropicsample_conditions_1
3D HNCOtriple_labeled_pMHC-Iisotropicsample_conditions_1
3D HN(CA)CBtriple_labeled_pMHC-Iisotropicsample_conditions_1
3D 1H-15N NOESYAILV_methyl_pMHC-Iisotropicsample_conditions_1
3D Hm-CmHm SOFAST NOESY HMQCAILV_methyl_pMHC-Iisotropicsample_conditions_1
2D 1H-13C SOFAST HMQCAILV_methyl_pMHC-Iisotropicsample_conditions_1
3D Cm-CmHm SOFAST HMQC NOESY HMQCAILV_methyl_pMHC-Iisotropicsample_conditions_1
3D Hn-CmHm SOFAST NOESY HMQCAILV_methyl_pMHC-Iisotropicsample_conditions_1
3D Cm-NHn SOFAST HMQC NOESY HMQCAILV_methyl_pMHC-Iisotropicsample_conditions_1
3D HMCM[CG]CBCAILV*_pMHC-Iisotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

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