BMRB Entry 17378

Name: Structure of CEL-PEP-RAGE V domain complex
Published: 2011-05-18

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PDB ID: 2l7u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17378
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of CEL-PEP-RAGE V domain complex

Deposition date:

2010-12-23

Original release date:

2011-05-18

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:

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).
PubMed: 21565706

Assembly members:

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:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	345
15N chemical shifts	92
1H chemical shifts	656

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	v_domain	1
2	CEL-PEP	2
3	4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE	3

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

GLY

SER

ALA

GLN

ASN

ILE

THR

ALA

ARG

ILE

2

GLY

GLU

PRO

LEU

VAL

LEU

LYS

CYS

LYS

GLY

3

ALA

PRO

LYS

PRO

GLN

ARG

LEU

GLU

4

TRP

LYS

LEU

ASN

THR

GLY

ARG

THR

GLU

ALA

5

TRP

LYS

VAL

LEU

SER

PRO

GLN

GLY

6

PRO

TRP

ASP

SER

VAL

ALA

ARG

VAL

LEU

PRO

7

ASN

GLY

SER

LEU

PHE

LEU

PRO

ALA

VAL

GLY

8

ILE

GLN

ASP

GLU

GLY

ILE

PHE

ARG

CYS

GLN

9

ALA

MET

ASN

ARG

ASN

GLY

LYS

GLU

THR

LYS

10

SER

ASN

TYR

ARG

VAL

ARG

VAL

TYR

GLN

ILE

11

PRO

GLY

LYS

PRO

GLU

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

ASP

GLU

PHE

CEL

ALA

ASP

GLU

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample-2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample-2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample-2	isotropic	sample_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

BMRB	19739 19953
PDB	2E5E 2L7U 2M1K 2MJW 2MOV 3CJJ 3O3U 4LP4 4LP5 4OF5 4OFV 4OI7 4OI8 4P2Y
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
AlphaFold	Q15109 Q3SZR2