BMRB Entry 30726

Name: Structure of the C-terminal Domain of RAGE and Its Inhibitor
Published: 2021-02-20

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PDB ID: 6vxg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30726
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the C-terminal Domain of RAGE and Its Inhibitor

Deposition date:

2020-02-21

Original release date:

2021-02-20

Authors:

Ramirez, L.; Shekhtman, A.

Citation:

Citation: Manigrasso, Michaele; Rabbani, Piul; Egana-Gorrono, Lander; Quadri, Nosirudeen; Frye, Laura; Zhou, Boyan; Reverdatto, Sergey; Ramirez, Lisa; Dansereau, Stephen; Pan, Jinhong; Li, Huilin; D'Agati, Vivette; Ramasamy, Ravichandran; DeVita, Robert; Shekhtman, Alexander; Schmidt, Ann. "Small-molecule antagonism of the interaction of the RAGE cytoplasmic domain with DIAPH1 reduces diabetic complications in mice" Sci. Transl. Med. 13, eabf7084-eabf7084 (2021).
PubMed: 34818060

Assembly members:

Assembly members:
entity_1, polymer, 43 residues, 5035.241 Da.
entity_RQV, non-polymer, 388.462 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MWQRRQRRGEERKAPENQEE EEERAELNQSEEPEAGESST GGP

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	112
15N chemical shifts	40
1H chemical shifts	231

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 43 residues - 5035.241 Da.

1

MET

TRP

GLN

ARG

GLN

ARG

GLY

GLU

2

GLU

ARG

LYS

ALA

PRO

GLU

ASN

GLN

GLU

3

GLU

ARG

ALA

GLU

LEU

ASN

GLN

SER

4

GLU

PRO

GLU

ALA

GLY

GLU

SER

THR

5

GLY

PRO

Entity 2, unit_2 - C23 H24 N4 O2 - 388.462 Da.

1

RQV

Samples:

sample_1: C-terminal RAGE, [U-100% 13C; U-100% 15N], 300 uM; potassium phosphate 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCCONH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.98.5, Guntert P. - refinement, structure calculation

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE 600 MHz

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