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- PDB-5d7f: X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide -

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Basic information

Entry
Database: PDB / ID: 5d7f
TitleX-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-B
KeywordsPROTEIN BINDING / metal binding protein / membrane protein
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 / adaptive thermogenesis / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / sympathetic neuron projection extension / RAGE receptor binding / induction of positive chemotaxis / transcytosis / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / protein localization to membrane / regulation of long-term synaptic potentiation / positive regulation of p38MAPK cascade / 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 / regulation of neuronal synaptic plasticity / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / phagocytic cup / phagocytosis / transport across blood-brain barrier / Nuclear signaling by ERBB4 / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / positive regulation of neuron differentiation / axonogenesis / central nervous system development / 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 / positive regulation of non-canonical NF-kappaB signal transduction / regulation of synaptic plasticity / memory / tau protein binding / positive regulation of interleukin-6 production / response to wounding / fibrillar center / cellular response to amyloid-beta / neuron projection development / calcium-dependent protein binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cell junction / signaling receptor activity / amyloid-beta binding / microtubule cytoskeleton / regulation of inflammatory response / molecular adaptor activity / histone binding / positive regulation of canonical NF-kappaB signal transduction / learning or memory / response to hypoxia / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / cell adhesion / ciliary basal body / cilium / apical plasma membrane / inflammatory response / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Protein S100-B / 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 / EF hand domain ...: / Protein S100-B / 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 / EF hand 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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein S100-B / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsJensen, J.L. / Colbert, C.L.
CitationJournal: To Be Published
Title: X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide
Authors: Jensen, J.L. / Colbert, C.L.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-B
B: Protein S100-B
P: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,69413
Polymers22,9813
Non-polymers71310
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-89 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.089, 59.824, 47.563
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein S100-B / S-100 protein beta chain / S-100 protein subunit beta / S100 calcium-binding protein B


Mass: 10727.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Plasmid: pGEMEX-S100B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04271
#2: Protein/peptide Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 1526.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15109
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100mM Na cacodylate pH 6.8, 22% w/v PEG 3350, 5mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.17→44.2 Å / Num. obs: 58236 / % possible obs: 97.9 % / Redundancy: 3.2 % / Net I/σ(I): 23.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H61

2h61


Resolution: 1.3→44.2 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1832 1526 3.47 %Random
Rwork0.1573 ---
obs0.1583 43997 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 40 214 1809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141847
X-RAY DIFFRACTIONf_angle_d1.6712498
X-RAY DIFFRACTIONf_dihedral_angle_d13.626719
X-RAY DIFFRACTIONf_chiral_restr0.105265
X-RAY DIFFRACTIONf_plane_restr0.008326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3420.2261340.16613845X-RAY DIFFRACTION98
1.342-1.38990.17491380.1493846X-RAY DIFFRACTION98
1.3899-1.44560.18891410.13423900X-RAY DIFFRACTION100
1.4456-1.51140.16381370.12313874X-RAY DIFFRACTION99
1.5114-1.59110.16541370.12283810X-RAY DIFFRACTION96
1.5911-1.69080.1791400.12143897X-RAY DIFFRACTION100
1.6908-1.82130.18541400.13253915X-RAY DIFFRACTION99
1.8213-2.00460.15591390.14273773X-RAY DIFFRACTION96
2.0046-2.29470.14811380.13743909X-RAY DIFFRACTION99
2.2947-2.89090.1911400.17263840X-RAY DIFFRACTION97
2.8909-44.23380.20491420.18463833X-RAY DIFFRACTION95

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