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- PDB-2e5e: Solution Structure of Variable-type Domain of Human Receptor for ... -

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Basic information

Entry
Database: PDB / ID: 2e5e
TitleSolution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / VARIABLE-TYPE IMMUNOGLOBULIN-LIKE FOLD
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 / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression ...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 / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / 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 p38MAPK cascade / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / regulation of long-term synaptic potentiation / negative regulation of connective tissue replacement involved in inflammatory response wound healing / 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 / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / 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 / molecular adaptor activity / histone binding / response to hypoxia / learning or memory / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMatsumoto, S. / Yoshida, T. / Yasumatsu, I. / Yamamoto, H. / Kobayashi, Y. / Ohkubo, T.
CitationJournal: to be published
Title: Solution Structure of Variable-type Domain of Human Receptor for Advanced Glycation Endproducts
Authors: Matsumoto, S. / Yoshida, T. / Yasumatsu, I. / Yamamoto, H. / Kobayashi, Y. / Ohkubo, T.
History
DepositionDec 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)11,2171
Polymers11,2171
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)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11217.007 Da / Num. of mol.: 1 / Fragment: VARIABLE-TYPE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET32B / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B (DE3) / References: UniProt: Q15109
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1322D NOESY
1422D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM Variable-type Domain of Receptor for Advanced Glycation Endproducts U-15N, 13C; 20mM phosphate buffer NA, 100mM NA2SO4; 90% H2O, 10% D2O90% H2O/10% D2O
20.2mM Variable-type Domain of Receptor for Advanced Glycation Endproducts; 20mM phosphate buffer NA, 100mM NA2SO4; 100% D2O100% D2O
Sample conditionspH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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