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 17378

Title: Structure of CEL-PEP-RAGE V domain complex   PubMed: 21565706

Authors: Xue, Jing; Rai, Vivek; Schmidt, Ann-Marie; Frolov, Sergey; Reverdatto, Sergey; Singer, David; Chabierski, Stefan; Xie, Jingjing; Burz, David; Shekhtman, Alexander; Hoffman, Ralf

Citation: Xue, Jing; Rai, Vivek; Singer, David; Chabierski, Stefan; Xie, Jingjing; Reverdatto, Sergey; Burz, David; Schmidt, Ann Marie; Hoffmann, Ralf; Shekhtman, Alexander. "Advanced Glycation End Product Recognition by the Receptor for AGEs."  Structure 19, 722-732 (2011).

Assembly members:
V_domain, polymer, 105 residues, 11571.429 Da.
CEL-PEP, polymer, 7 residues, 724.677 Da.
MCL, polymer, . residues, 218.250 Da.

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

Entity Sequences (FASTA):
V_domain: GSAQNITARIGEPLVLKCKG APKKPPQRLEWKLNTGRTEA WKVLSPQGGGPWDSVARVLP NGSLFLPAVGIQDEGIFRCQ AMNRNGKETKSNYRVRVYQI PGKPE
CEL-PEP: DEFXADE

Data sets:
Data typeCount
13C chemical shifts345
15N chemical shifts92
1H chemical shifts656

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1v_domain1
2CEL-PEP2
34-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE3

Entities:

Entity 1, v_domain 105 residues - 11571.429 Da.

Residues 1-2 represent non-native affinity tag Residues 3-105 in the PDB file represent residues 23-123 of the V domain of RAGE.

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

Entity 2, CEL-PEP 7 residues - 724.677 Da.

This sequence contains a modified lysine, Nepsilon -carboxy-ethyl-lysine (CEL). The CEL is denoted by X.

1   ASPGLUPHECELALAASPGLU

Entity 3, 4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE - 218.250 Da.

1   MCL

Samples:

sample_1: V domain, [U-100% 13C; U-100% 15N], 0.1 mM; CEL-PEP 0.3 mM; H2O 90%; D2O 10%

sample-2: V domain, [U-100% 13C; U-100% 15N], 0.32 mM; CEL-PEP 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.130 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample-2isotropicsample_conditions_1
3D 1H-13C NOESYsample-2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample-2isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CARA, Bartels et al. - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 500 MHz

Related Database Links:

BMRB 19739 19953
PDB
DBJ BAA05958 BAA89369 BAC65465 BAG35995 BAG60385
GB AAA03574 AAB47491 AAH20669 AAX07272 AAX07273
REF NP_001127 NP_001192046 NP_001193858 NP_001193863 NP_001193865
SP Q15109