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- PDB-9d36: Structure of the C-terminal Domain of RAGE and Its Inhibitor -

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Basic information

Entry
Database: PDB / ID: 9d36
TitleStructure of the C-terminal Domain of RAGE and Its Inhibitor
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsPROTEIN BINDING/INHIBITOR / RAGE / AGE / Receptor for Advanced Glycation Endproducts / Inhibitor / ctRAGE / PROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation ...advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / transcytosis / induction of positive chemotaxis / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / positive regulation of monocyte chemotactic protein-1 production / positive regulation of p38MAPK cascade / regulation of long-term synaptic potentiation / negative regulation of connective tissue replacement involved in inflammatory response wound healing / protein localization to membrane / regulation of spontaneous synaptic transmission / scavenger receptor activity / laminin receptor activity / positive regulation of double-strand break repair / 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 / negative regulation of long-term synaptic potentiation / phagocytosis / phagocytic cup / transport across blood-brain barrier / positive regulation of chemokine production / positive regulation of interleukin-12 production / astrocyte activation / positive regulation of interleukin-1 beta production / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / regulation of synaptic plasticity / positive regulation of interleukin-6 production / response to wounding / fibrillar center / cellular response to amyloid-beta / neuron projection development / positive regulation of tumor necrosis factor production / cell junction / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / histone binding / molecular adaptor activity / learning or memory / response to hypoxia / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / apical plasma membrane / inflammatory response / protein-containing complex binding / cell surface / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set 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. ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set 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
: / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTheophall, G.G. / Ramasamy, R. / Schmidt, A.M. / Manigrasso, M. / Shekthman, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: Solution NMR Structure of ctRAGE bound to small molecule inhibitor
Authors: Theophall, G.G. / Ramasamy, R. / Schmidt, A.M. / Manigrasso, M. / Shekthman, A.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)5,4302
Polymers5,0171
Non-polymers4121
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 5017.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15109
#2: Chemical ChemComp-A1A2E / 4-[(morpholin-4-yl)methyl]-2-{4-[(2R)-5-oxopyrrolidin-2-yl]phenyl}quinoline-7-carbonitrile


Mass: 412.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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
181isotropic13D 1H-13C NOESY aromatic
171isotropic13D CBCA(CO)NH
1101isotropic13D (H)CCH-TOCSY
191isotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution140 uM [U-13C; U-15N] ctRAGE, 100 uM RAGE406R, 90% H2O/10% D2ODMSO was added at ~ 1% to compensate for small molecule solubility.13C_15N_ctRAGE+406R90% H2O/10% D2O
solution240 uM [U-13C; U-15N] ctRAGE, 90% H2O/10% D2ODMSO was added at ~ 1% to compensate for small molecule solubility.13C_15N_ctRAGE90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
40 uMctRAGE[U-13C; U-15N]1
100 uMRAGE406Rnatural abundance1
40 uMctRAGE[U-13C; U-15N]2
Sample conditionsIonic strength: 60 mM / Label: Standard / pH: 6.5 / 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 Cyroprobe

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARA20.12.24Elmar Krieger, Kornel Ozvoldik, Dr. Henk-Jan Joosten, Gert Vriendrefinement
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10000 / Conformers submitted total number: 20

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