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- PDB-2m1k: Interaction of Human S100A6 (C3S) with V domain of Receptor for A... -

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Basic information

Entry
Database: PDB / ID: 2m1k
TitleInteraction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products (RAGE)
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A6
KeywordsPROTEIN BINDING / S100A6 C3S / RAGE V / heterotetrameric / HADDOCK model
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / 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 / monoatomic ion transmembrane transporter activity ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / 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 / monoatomic ion transmembrane transporter activity / 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 / laminin receptor activity / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / tropomyosin binding / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / axonogenesis / 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 / cytoplasmic side of plasma membrane / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / calcium-dependent protein binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / positive regulation of fibroblast proliferation / cell junction / nuclear envelope / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / collagen-containing extracellular matrix / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / signal transduction / protein homodimerization activity / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / 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 / Immunoglobulin domain ...Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / 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 / Immunoglobulin domain / Immunoglobulin domain / EF-hand / Recoverin; domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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
Protein S100-A6 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGupta, A.A. / Yu, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Interaction of the S100A6 mutant (C3S) with the V domain of the receptor for advanced glycation end products (RAGE).
Authors: Mohan, S.K. / Gupta, A.A. / Yu, C.
History
DepositionNov 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein S100-A6
D: Protein S100-A6
A: Advanced glycosylation end product-specific receptor
C: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)42,7894
Polymers42,7894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area23380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-A6 / Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / ...Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / PRA / S100 calcium-binding protein A6


Mass: 10177.664 Da / Num. of mol.: 2 / Mutation: C3S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACY, S100A6 / Plasmid: pET(20b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06703
#2: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 11217.007 Da / Num. of mol.: 2 / Fragment: UNP residues 23-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pET(15b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15109

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products
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 HNCO
1713D HCACO

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] S100A6 C3S, 20 mM TRIS, 10 mM Calcium chloride, 0.01 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMS100A6 C3S-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
10 mMCalcium chloride-31
0.01 %sodium azide-41
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3Variancollection
VnmrJ2.3Varianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: HADDOCK STARTING STRUCTURES ARE PDB ENTRIES 1K9K AND 2E5E. MODELS 1-10 ARE SUPERIMPOSED, WHILE MODELS 11-20 ARE SUPERIMPOSED IN A DIFFERENT ORIENTATION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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