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- PDB-6vxg: Structure of the C-terminal Domain of RAGE and Its Inhibitor -

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Basic information

Entry
Database: PDB / ID: 6vxg
TitleStructure of the C-terminal Domain of RAGE and Its Inhibitor
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN/INHIBITOR / Inhibitor / Complex / Diabetes / Receptor for Advanced Glycated End Products / Inflammation / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation ...regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / laminin receptor activity / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / positive regulation of interleukin-6 production / transmembrane signaling receptor activity / neuron projection development / positive regulation of tumor necrosis factor production / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / apical plasma membrane / positive regulation of protein phosphorylation / protein-containing complex binding / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-RQV / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRamirez, L. / Shekhtman, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL146367 United States
Citation
Journal: Sci Transl Med / Year: 2021
Title: Small-molecule antagonism of the interaction of the RAGE cytoplasmic domain with DIAPH1 reduces diabetic complications in mice.
Authors: Manigrasso, M.B. / Rabbani, P. / Egana-Gorrono, L. / Quadri, N. / Frye, L. / Zhou, B. / Reverdatto, S. / Ramirez, L.S. / Dansereau, S. / Pan, J. / Li, H. / D'Agati, V.D. / Ramasamy, R. / ...Authors: Manigrasso, M.B. / Rabbani, P. / Egana-Gorrono, L. / Quadri, N. / Frye, L. / Zhou, B. / Reverdatto, S. / Ramirez, L.S. / Dansereau, S. / Pan, J. / Li, H. / D'Agati, V.D. / Ramasamy, R. / DeVita, R.J. / Shekhtman, A. / Schmidt, A.M.
#1: Journal: J. Biol. Chem. / Year: 2012
Title: Signal transduction in receptor for advanced glycation end products (RAGE): solution structure of C-terminal rage (ctRAGE) and its binding to mDia1.
Authors: Rai, V. / Maldonado, A.Y. / Burz, D.S. / Reverdatto, S. / Yan, S.F. / Schmidt, A.M. / Shekhtman, A.
History
DepositionFeb 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4222
Polymers5,0351
Non-polymers3861
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 5035.241 Da / Num. of mol.: 1 / Fragment: C-terminal residues 363-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15109
#2: Chemical ChemComp-RQV / N-(4-{7-cyano-4-[(morpholin-4-yl)methyl]quinolin-2-yl}phenyl)acetamide


Mass: 386.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
161isotropic13D 1H-15N TOCSY
171isotropic13D 1H-13C NOESY aromatic
181isotropic13D CBCA(CO)NH
191isotropic13D (H)CC(CO)NH
1101isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] C-terminal RAGE, 90% H2O/10% D2O
Details: Recombinant protein bound to small molecule ligand (N-(4-(7-cyano-4-(morpholin-4-ylmethyl)quinoline-2-yl)phenyl)acetamide)
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: C-terminal RAGE / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 10 mM potassium phosphate buffer, pH 7.0 / Ionic strength: 10 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: QCI HCN cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.5Guntert P.refinement
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
CYANA3.98.5Guntert P.structure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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