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 19120

Title: Chemical shifts of human beta-2 microglobulin bound to HLA-B2705 complexed with the nonamer peptide pVIPR (RRKWRRWHL)   PubMed: 24006098

Deposition date: 2013-03-27 Original release date: 2014-01-02

Authors: Beerbaum, Monika; Ballaschk, Martin; Erdmann, Natalja; Schnick, Christina; Diehl, Anne; Uchanska-Ziegler, Barbara; Ziegler, Andreas; Schmieder, Peter

Citation: Beerbaum, Monika; Ballaschk, Martin; Erdmann, Natalja; Schnick, Christina; Diehl, Anne; Uchanska-Ziegler, Barbara; Ziegler, Andreas; Schmieder, Peter. "NMR spectroscopy reveals unexpected structural variation at the protein-protein interface in MHC class I molecules."  J. Biomol. NMR 57, 167-178 (2013).

Assembly members:
human_beta-2_microglobulin, polymer, 100 residues, Formula weight is not available
pVIPR_peptide, polymer, 9 residues, Formula weight is not available
HLA-B2705, polymer, 276 residues, Formula weight is not available

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pHN1+

Entity Sequences (FASTA):
human_beta-2_microglobulin: MIQRTPKIQVYSRHPAENGK SNFLNCYVSGFHPSDIEVDL LKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYA CRVNHVTLSQPKIVKWDRDM
pVIPR_peptide: RRKWRRWHL
HLA-B2705: GSHSMRYFHTSVSRPGRGEP RFITVGYVDDTLFVRFDSDA ASPREEPRAPWIEQEGPEYW DRETQICKAKAQTDREDLRT LLRYYNQSEAGSHTLQNMYG CDVGPDGRLLRGYHQHAYDG KDYIALNEDLSSWTAADTAA QITQRKWEAARVAEQLRAYL EGECVEWLRRYLENGKETLQ RADPPKTHVTHHPISDHEAT LRCWALGFYPAEITLTWQRD GEDQTQDTELVETRPAGDRT FQKWAAVVVPSGEEQRYTCH VQHEGLPKPLTLRWEP

Data sets:
Data typeCount
15N chemical shifts79
1H chemical shifts79

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1beta-2 microglobulin1
2pVIPR peptide2
3HLA-B2705 protein3

Entities:

Entity 1, beta-2 microglobulin 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

Entity 2, pVIPR peptide 9 residues - Formula weight is not available

1   ARGARGLYSTRPARGARGTRPHISLEU

Entity 3, HLA-B2705 protein 276 residues - Formula weight is not available

1   GLYSERHISSERMETARGTYRPHEHISTHR
2   SERVALSERARGPROGLYARGGLYGLUPRO
3   ARGPHEILETHRVALGLYTYRVALASPASP
4   THRLEUPHEVALARGPHEASPSERASPALA
5   ALASERPROARGGLUGLUPROARGALAPRO
6   TRPILEGLUGLNGLUGLYPROGLUTYRTRP
7   ASPARGGLUTHRGLNILECYSLYSALALYS
8   ALAGLNTHRASPARGGLUASPLEUARGTHR
9   LEULEUARGTYRTYRASNGLNSERGLUALA
10   GLYSERHISTHRLEUGLNASNMETTYRGLY
11   CYSASPVALGLYPROASPGLYARGLEULEU
12   ARGGLYTYRHISGLNHISALATYRASPGLY
13   LYSASPTYRILEALALEUASNGLUASPLEU
14   SERSERTRPTHRALAALAASPTHRALAALA
15   GLNILETHRGLNARGLYSTRPGLUALAALA
16   ARGVALALAGLUGLNLEUARGALATYRLEU
17   GLUGLYGLUCYSVALGLUTRPLEUARGARG
18   TYRLEUGLUASNGLYLYSGLUTHRLEUGLN
19   ARGALAASPPROPROLYSTHRHISVALTHR
20   HISHISPROILESERASPHISGLUALATHR
21   LEUARGCYSTRPALALEUGLYPHETYRPRO
22   ALAGLUILETHRLEUTHRTRPGLNARGASP
23   GLYGLUASPGLNTHRGLNASPTHRGLULEU
24   VALGLUTHRARGPROALAGLYASPARGTHR
25   PHEGLNLYSTRPALAALAVALVALVALPRO
26   SERGLYGLUGLUGLNARGTYRTHRCYSHIS
27   VALGLNHISGLUGLYLEUPROLYSPROLEU
28   THRLEUARGTRPGLUPRO

Samples:

sample_1: beta-2 microglobulin, [U-13C; U-15N], 0.42 mM; pVIPR peptide 0.42 mM; HLA-B2705 protein 0.42 mM; Sodium Phosphate 10 mM; Sodium Chloride 150 mM

sample_conditions_1: ionic strength: 160 mM; pH: 7.5; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCACOsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.1 -

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 750 MHz

Related Database Links:

BMRB 15480 16587 17165 17166 19099 19113 19116 19118 19119 19121 19122 19123 3078 3079 19113 19116 19118 19119 19121 19122 19123
PDB
DBJ BAA35182 BAG38125 BAG64583 BAG72952 BAA11753 BAJ83633 BAN59815
EMBL CAA23830 CAG33347 CAH92078 CAA27301 CAA27302 CAA27578 CAA51980 CAA83876
GB AAA51811 AAA87972 AAA88008 AAB25312 AAB35347 AAA36221 AAA59614 AAA59616 AAA59643 AAA59647
REF NP_001009066 NP_001127503 NP_004039 XP_003266898 XP_004056148
SP P16213 P61769 P61770 P61771 P03989
PRF 1413302A
AlphaFold P61771 P61770 P61769 P16213 P03989

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