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- PDB-7quv: Crystal structure of human Calprotectin (S100A8/S100A9) in comple... -

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Basic information

Entry
Database: PDB / ID: 7quv
TitleCrystal structure of human Calprotectin (S100A8/S100A9) in complex with Peptide 3
Components
  • (Protein S100- ...) x 2
  • Peptide 3
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / regulation of respiratory burst involved in inflammatory response / modulation of process of another organism / autocrine signaling / Toll-like receptor 4 binding ...S100A9 complex / regulation of integrin biosynthetic process / sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / 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 / peptide secretion / leukocyte migration involved in inflammatory response / RAGE receptor binding / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / intermediate filament cytoskeleton / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / response to zinc ion / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / peptidyl-cysteine S-nitrosylation / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / response to ethanol / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol
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
Chem-F3U / : / AMINO GROUP / NICKEL (II) ION / TRIETHYLENE GLYCOL / Protein S100-A8 / Protein S100-A9
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDiaz-Perlas, C. / Heinis, C. / Pojer, F. / Lau, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays.
Authors: Diaz-Perlas, C. / Ricken, B. / Farrera-Soler, L. / Guschin, D. / Pojer, F. / Lau, K. / Gerhold, C.B. / Heinis, C.
History
DepositionJan 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein S100-A9
A: Protein S100-A8
C: Peptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,16114
Polymers27,2393
Non-polymers92211
Water1,63991
1
B: Protein S100-A9
A: Protein S100-A8
C: Peptide 3
hetero molecules

B: Protein S100-A9
A: Protein S100-A8
C: Peptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32128
Polymers54,4786
Non-polymers1,84322
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area15990 Å2
ΔGint-212 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.789, 50.789, 148.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein S100- ... , 2 types, 2 molecules BA

#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: 14131.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14 / Production host: Escherichia coli (E. coli) / References: UniProt: P06702
#2: Protein Protein S100-A8 / Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex ...Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex light chain / Migration inhibitory factor-related protein 8 / MRP-8 / p8 / S100 calcium-binding protein A8 / Urinary stone protein band A


Mass: 10991.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A8, CAGA, CFAG, MRP8 / Production host: Escherichia coli (E. coli) / References: UniProt: P05109

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Peptide 3


Mass: 2115.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 10 types, 102 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-F3U / 4-methanoyl-2-(6-oxidanyl-3-oxidanylidene-4~{H}-xanthen-9-yl)benzoic acid


Mass: 360.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H12O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), 25% w/v PEG 1500, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.98 Å / Num. obs: 35628 / % possible obs: 97.64 % / Redundancy: 10.5 % / Biso Wilson estimate: 25.62 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 21.68
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 2772 / Rrim(I) all: 0.797

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GGF

4ggf


Resolution: 1.85→43.98 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2752 3530 9.91 %
Rwork0.2206 32098 -
obs0.226 35628 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 54 91 1900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921860
X-RAY DIFFRACTIONf_angle_d1.01532494
X-RAY DIFFRACTIONf_chiral_restr0.0523257
X-RAY DIFFRACTIONf_plane_restr0.0094316
X-RAY DIFFRACTIONf_dihedral_angle_d8.2163239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.46191440.40941365X-RAY DIFFRACTION96.11
1.87-1.90.53651050.467942X-RAY DIFFRACTION74.26
1.9-1.930.63881380.58791255X-RAY DIFFRACTION97.69
1.93-1.960.38011170.42471196X-RAY DIFFRACTION85.48
1.96-1.990.35311460.30341281X-RAY DIFFRACTION99.86
1.99-2.030.32841470.29621336X-RAY DIFFRACTION99.33
2.03-2.060.29971520.28851320X-RAY DIFFRACTION99.59
2.06-2.10.30241410.25871298X-RAY DIFFRACTION98.97
2.1-2.140.32811520.23871309X-RAY DIFFRACTION99.8
2.14-2.190.3011460.22661333X-RAY DIFFRACTION99.73
2.19-2.240.40841190.37691138X-RAY DIFFRACTION85.8
2.24-2.30.56341180.40431135X-RAY DIFFRACTION86
2.3-2.360.22841400.22131336X-RAY DIFFRACTION99.39
2.36-2.430.29111450.22561313X-RAY DIFFRACTION99.79
2.43-2.510.26561460.2061322X-RAY DIFFRACTION99.59
2.51-2.60.28031390.21891317X-RAY DIFFRACTION99.79
2.6-2.70.25741500.20061325X-RAY DIFFRACTION99.86
2.7-2.820.23681570.21021329X-RAY DIFFRACTION100
2.83-2.970.27691480.22631310X-RAY DIFFRACTION100
2.97-3.160.3291520.20551324X-RAY DIFFRACTION100
3.16-3.40.27971380.18351344X-RAY DIFFRACTION100
3.4-3.740.27361320.17981309X-RAY DIFFRACTION99.24
3.75-4.290.2011450.15431330X-RAY DIFFRACTION100
4.29-5.40.19061540.15571310X-RAY DIFFRACTION100
5.41-43.980.20441590.17531321X-RAY DIFFRACTION100

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