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- PDB-7ui5: Evolution avoids a pathological stabilizing interaction in the im... -

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Basic information

Entry
Database: PDB / ID: 7ui5
TitleEvolution avoids a pathological stabilizing interaction in the immune protein S100A9
ComponentsProtein S100-A9
KeywordsSIGNALING PROTEIN / S100A9 / calcium binding / S100 / signaling
Function / homology
Function and homology information


regulation of integrin biosynthetic process / S100A9 complex / sequestering of zinc ion / neutrophil aggregation / calprotectin complex / modulation of process of another organism / regulation of respiratory burst involved in inflammatory response / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation ...regulation of integrin biosynthetic process / S100A9 complex / sequestering of zinc ion / neutrophil aggregation / calprotectin complex / modulation of process of another organism / regulation of respiratory burst involved in inflammatory response / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Metal sequestration by antimicrobial proteins / Toll-like receptor 4 binding / RAGE receptor binding / leukocyte migration involved in inflammatory response / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonate 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 / endothelial cell migration / RHO GTPases Activate NADPH Oxidases / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / : / positive regulation of neuron projection development / autophagy / positive regulation of inflammatory response / 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 / microtubule binding / positive regulation of cell growth / collagen-containing extracellular matrix / secretory granule lumen / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / calcium ion binding / Neutrophil degranulation / apoptotic process / 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, 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsReardon, P.N. / Harman, J.L. / Costello, S.M. / Warren, G.D. / Phillips, S.R. / Connor, P.J. / Marqusee, S. / Harms, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117140 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-T32GM007413 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Evolution avoids a pathological stabilizing interaction in the immune protein S100A9.
Authors: Harman, J.L. / Reardon, P.N. / Costello, S.M. / Warren, G.D. / Phillips, S.R. / Connor, P.J. / Marqusee, S. / Harms, M.J.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6886
Polymers26,5282
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures 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 / MRP-14 / p14 / S100 calcium-binding protein A9


Mass: 13263.934 Da / Num. of mol.: 2 / Mutation: C3S/M63F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06702
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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
121isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic1HN(CO)CACB
181isotropic13D 1H-13C 1H-15N NOESY
191isotropic13D HNHA
1101isotropic12D HDCB
1111isotropic12D HECB
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 25 mM TRIS, 100 mM sodium chloride, 10 mM calcium chloride, 1 mM [U-100% 13C; U-100% 15N] S100A9-M63F, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
10 mMcalcium chloridenatural abundance1
1 mMS100A9-M63F[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 110 mM / Label: 15N_13C_sample / pH: 7.4 / Pressure: 1.01 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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