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- PDB-2le9: RAGEC2-S100A13 tetrameric complex -

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Basic information

Entry
Database: PDB / ID: 2le9
TitleRAGEC2-S100A13 tetrameric complex
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A13
KeywordsMEMBRANE PROTEIN/METAL BINDING PROTEIN / Receptor for Advanced Glycation End products / S100A13 / tetrameric complex / MEMBRANE PROTEIN-METAL BINDING PROTEIN complex
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 / positive regulation of interleukin-1 alpha production / RAGE receptor binding / 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 / mast cell degranulation / negative regulation of interleukin-10 production / fibroblast growth factor binding / 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 / positive regulation of cytokine 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 / calcium-dependent protein binding / positive regulation of tumor necrosis factor production / neuron projection development / transmembrane signaling receptor activity / protein transport / cell junction / positive regulation of NF-kappaB transcription factor activity / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / 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 / copper ion binding / lipid binding / positive regulation of cell population proliferation / calcium ion binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / EF-hand / Recoverin; domain 1 ...: / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / EF-hand / Recoverin; domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Advanced glycosylation end product-specific receptor / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsRani, S.G. / Mohan, S.K. / Yu, C.
CitationJournal: To be Published
Title: Interaction of S100A13 with Receptor for Advanced Glycation End products (RAGE) C2 domain
Authors: Rani, S.G. / Mohan, S.K. / Yu, C.
History
DepositionJun 14, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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_software.name
Revision 1.2Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor
B: Protein S100-A13
C: Protein S100-A13
D: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)42,0104
Polymers42,0104
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)1 / 4000structures with the lowest energy
Representative

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Components

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


Mass: 9645.792 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 235-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE, RAGEC2 / Variant: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q15109
#2: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11358.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Variant: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q99584
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
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D 13C-Filter NOESY
21322D 1H-15N HSQC
21423D HNCA
21523D HN(CO)CA
21623D HN(CA)CB
21723D CBCA(CO)NH
21823D C(CO)NH
21923D H(CCO)NH
22023D HBHA(CO)NH
22123D 1H-15N NOESY
22223D 1H-13C NOESY
22323D HNCO
224213C Filter NOESY
12513D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.1 mM entity_2-2, 25 mM sodium phosphate-3, 100 mM sodium chloride-4, 1 mM DTT-5, 0.02 mM sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM entity_1-7, 1.2 mM [U-100% 13C; U-100% 15N] entity_2-8, 25 mM sodium phosphate-9, 100 mM sodium chloride-10, 1 mM DTT-11, 0.02 mM sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMentity_1-1[U-100% 13C; U-100% 15N]1
1.1 mMentity_2-21
25 mMsodium phosphate-31
100 mMsodium chloride-41
1 mMDTT-51
0.02 mMsodium azide-61
1.2 mMentity_1-72
1.2 mMentity_2-8[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-92
100 mMsodium chloride-102
1 mMDTT-112
0.02 mMsodium azide-122
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11006.5ambient 298 K
21006.5ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7001
Varian INOVAVarianINOVA7002
Varian INOVAVarianINOVA7003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
HADDOCK2Alexandre Bonvincomplex structure
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
VNMRVariancollection
VNMRVarianprocessing
TALOSCornilescu, Delaglio and Baxdihedral angles
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 1 / Representative conformer: 1

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