BMRB Entry 19953

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR19953
MolProbity Validation Chart

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Title:
Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal Derived AGEs.
Deposition date:
2014-05-05
Original release date:
2014-06-23
Authors:
Shekhtman, Alexander; Xue, Jing; Ray, Rasmi; Singer, David; Bohme, David; Burz, David; Rai, Vivek; Hoffman, Ralf
Citation:

Citation: Xue, Jing; Ray, Rasmi; Singer, David; Bohme, David; Burz, David; Rai, Vivek; Hoffman, Ralf; Shekhtman, Alexander. "The Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal-Derived AGEs"  Biochemistry 53, 3327-3335 (2014).
PubMed: 24824951

Assembly members:

Assembly members:
V_domain, polymer, 105 residues, 11571.429 Da.
N~5~-[(2S,4S,5R)-4-hydroxy-5-methylimidazolidin-2-yl]-L-ornithine, non-polymer, 232.280 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: pET28-V

Entity Sequences (FASTA):

Entity Sequences (FASTA):
V_domain: GSAQNITARIGEPLVLKCKG APKKPPQRLEWKLNTGRTEA WKVLSPQGGGPWDSVARVLP NGSLFLPAVGIQDEGIFRCQ AMNRNGKETKSNYRVRVYQI PGKPE

Data sets:
Data typeCount
1H chemical shifts623
13C chemical shifts345
15N chemical shifts92

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1V_domain1
2IOR2

Entities:

Entity 1, V_domain 105 residues - 11571.429 Da.

Residues 1-3 represent a non-native affinity tag.

1   GLYSERALAGLNASNILETHRALAARGILE
2   GLYGLUPROLEUVALLEULYSCYSLYSGLY
3   ALAPROLYSLYSPROPROGLNARGLEUGLU
4   TRPLYSLEUASNTHRGLYARGTHRGLUALA
5   TRPLYSVALLEUSERPROGLNGLYGLYGLY
6   PROTRPASPSERVALALAARGVALLEUPRO
7   ASNGLYSERLEUPHELEUPROALAVALGLY
8   ILEGLNASPGLUGLYILEPHEARGCYSGLN
9   ALAMETASNARGASNGLYLYSGLUTHRLYS
10   SERASNTYRARGVALARGVALTYRGLNILE
11   PROGLYLYSPROGLU

Entity 2, IOR - 232.280 Da.

1   IOR

Samples:

sample_1: V_domain, [U-13C; U-15N], 0.1 mM; IOR, [U-13C; U-15N], 0.1 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: temperature: 298 K; pH: 6.5; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HCACOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

REF NP_001127 NP_001127 NP_001192046 NP_001193858 NP_001193863 NP_001193865
BMRB 17378 19739
PDB
DBJ BAA05958 BAA89369 BAC65465 BAG35995 BAG60385
GB AAA03574 AAB47491 AAH20669 AAX07272 AAX07273
SP Q15109
AlphaFold Q15109

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