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- PDB-2lmb: Solution Structure of C-terminal RAGE (ctRAGE) -

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Basic information

Entry
Database: PDB / ID: 2lmb
TitleSolution Structure of C-terminal RAGE (ctRAGE)
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / Signal Transduction Receptor / cytosolic tail
Function / homology
Function and homology information


negative regulation of blood circulation / regulation of CD4-positive, alpha-beta T cell activation / positive regulation of endothelin production / advanced glycation end-product receptor activity / regulation of T cell mediated cytotoxicity / 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 ...negative regulation of blood circulation / regulation of CD4-positive, alpha-beta T cell activation / positive regulation of endothelin production / advanced glycation end-product receptor activity / regulation of T cell mediated cytotoxicity / 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 / 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 / laminin receptor activity / 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 / transport across blood-brain barrier / 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 interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / neuron projection development / transmembrane signaling receptor activity / cell junction / positive regulation of NF-kappaB transcription factor activity / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / 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 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
Model detailslowest energy, model 1
AuthorsRai, V. / Maldonado, A.Y. / Burz, D.S. / Reverdatto, S. / Schmidt, A. / Shekhtman, A.
CitationJournal: 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. / Schmidt, A.M. / Shekhtman, A.
History
DepositionNov 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
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
Revision 1.4May 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:
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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)5,0351
Polymers5,0351
Non-polymers00
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 #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: residues 363-404
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] ctRAGE, 10 % [U-100% 2H] D2O, 10 mM potassium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMctRAGE-1[U-99% 13C; U-99% 15N]1
10 %D2O-2[U-100% 2H]1
10 mMpotassium phosphate-31
100 mMsodium chloride-41
0.02 %sodium azide-51
Sample conditionsIonic strength: 130 / pH: 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 softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 295 / NOE intraresidue total count: 82 / NOE long range total count: 24 / NOE medium range total count: 41 / NOE sequential total count: 148 / Protein phi angle constraints total count: 33 / Protein psi angle constraints total count: 33
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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