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- PDB-2mjw: Structural Insights into Calcium Bound S100P - V Domain of the re... -

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Basic information

Entry
Database: PDB / ID: 2mjw
TitleStructural Insights into Calcium Bound S100P - V Domain of the receptor for advanced glycation end products (RAGE) Complex
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-P
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / S100P V Domain of RAGE / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
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 / positive regulation of dendritic cell differentiation ...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 / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / 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 / laminin receptor activity / positive regulation of p38MAPK cascade / microvillus membrane / 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 / transition metal ion binding / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / endothelial cell migration / positive regulation of chemokine production / positive regulation of interleukin-12 production / : / positive regulation of interleukin-1 beta production / sarcoplasmic reticulum / 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 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 / neuron projection development / positive regulation of tumor necrosis factor production / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / learning or memory / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / response to hypoxia / inflammatory response / cadherin binding / positive regulation of protein phosphorylation / apical plasma membrane / calcium ion binding / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / magnesium ion binding / protein homodimerization activity / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
S-100 / 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 ...S-100 / 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 calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein S100-P / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsRao, P.S.
CitationJournal: Plos One / Year: 2014
Title: Structural insights into calcium-bound S100P and the V domain of the RAGE complex.
Authors: Penumutchu, S.R. / Chou, R.H. / Yu, C.
History
DepositionJan 19, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: 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
A: Advanced glycosylation end product-specific receptor
B: Protein S100-P
D: Protein S100-P
C: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)42,9994
Polymers42,9994
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)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109
#2: Protein Protein S100-P / Migration-inducing gene 9 protein / MIG9 / Protein S100-E / S100 calcium-binding protein P


Mass: 10282.704 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100P, S100E / Production host: Escherichia coli (E. coli) / References: UniProt: P25815

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D HBHA(CO)NH
1913D 1H-13C NOESY
11013D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] entity_1-1, 0.6 mM [U-100% 13C; U-100% 15N] entity_2-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity_1-1[U-100% 13C; U-100% 15N]1
0.6 mMentity_2-2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.1 / pH: 6.8 / 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
NameDeveloperClassification
SparkyGoddardchemical shift assignment
HADDOCKrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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