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- PDB-2mov: Receptor for Advanced Glycation End Products (RAGE) Specifically ... -

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Basic information

Entry
Database: PDB / ID: 2mov
TitleReceptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal Derived AGEs.
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsPROTEIN BINDING / PROTEIN/LIGAND
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 / early endosome / response to hypoxia / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-IOR / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model12
AuthorsShekhtman, A. / Xue, J. / Ray, R. / Singer, D. / Bohme, D. / Burz, D.S. / Rai, V. / Hoffman, R.
CitationJournal: Biochemistry / Year: 2014
Title: The Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal-Derived AGEs.
Authors: Xue, J. / Ray, R. / Singer, D. / Bohme, D. / Burz, D.S. / Rai, V. / Hoffmann, R. / Shekhtman, A.
History
DepositionMay 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)11,8002
Polymers11,5711
Non-polymers2281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #12fewest violations

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Components

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


Mass: 11571.323 Da / Num. of mol.: 1 / Fragment: UNP residues 23-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109
#2: Chemical ChemComp-IOR / N~5~-[(5R)-5-methyl-4-oxo-4,5-dihydro-1H-imidazol-2-yl]-L-ornithine


Type: L-peptide linking / Mass: 228.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4O3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HNCO
1713D 1H-13C NOESY aromatic
1813D HCACO
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.1 mM [U-13C; U-15N] Methylglyoxal-derived hydroimidazolones isoform 1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.1 mM
Component: Methylglyoxal-derived hydroimidazolones isoform 1-1
Isotopic labeling: [U-13C; U-15N]
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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