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- PDB-5i8n: Solution Structure of human calcium-binding S100A9 (C3S) protein -

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Basic information

Entry
Database: PDB / ID: 5i8n
TitleSolution Structure of human calcium-binding S100A9 (C3S) protein
ComponentsProtein S100-A9
KeywordsMETAL BINDING PROTEIN / calgranulin B / homodimer / calcium-binding / migration inhibitory factor-related protein 14 (MRP14)
Function / homology
Function and homology information


S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response ...S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Metal sequestration by antimicrobial proteins / leukocyte migration involved in inflammatory response / Regulation of TLR by endogenous ligand / RAGE receptor binding / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / antioxidant activity / RHO GTPases Activate NADPH Oxidases / endothelial cell migration / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / autophagy / positive regulation of neuron projection development / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / collagen-containing extracellular matrix / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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 / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsChang, C.-C. / Chin, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST 103-2113-M-007 -017 -MY3 Taiwan
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation
Authors: Chang, C.-C. / Khan, I. / Tsai, K.-L. / Li, H. / Yang, L.-W. / Chou, R.-H. / Yu, C.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status / pdbx_nmr_software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A9
B: Protein S100-A9


Theoretical massNumber of molelcules
Total (without water)26,4962
Polymers26,4962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4620 Å2
ΔGint-37 kcal/mol
Surface area11220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-A9 / Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory ...Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / p14 / S100 calcium-binding protein A9


Mass: 13247.955 Da / Num. of mol.: 2 / Mutation: C3S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P06702

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
1101isotropic13D HNCO
191isotropic13D HN(CA)CO
181isotropic13D C(CO)NH
171isotropic13D H(CCO)NH
161isotropic13D (H)CCH-TOCSY
1141isotropic13D HBHA(CO)NH
1131isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 50 mM TRIS, 100 mM sodium chloride, 2 mM calcium chloride, 2 mM [U-13C; U-15N] S100A9 protein (C3S), , 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
2 mMcalcium chloridenatural abundance1
2 mMS100A9 protein (C3S)[U-13C; U-15N]1
Sample conditionsIonic strength: 0.1 M / Label: conditions_1 / pH: 7.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 310 K / Temperature err: 0.2

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3Varianprocessing
Sparky3.1Goddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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