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- PDB-9asx: BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by... -

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Basic information

Entry
Database: PDB / ID: 9asx
TitleBIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap3 of S. aureus
Components
  • Cathepsin-G
  • Extracellular Adherence Protein
  • Neutrophil elastase
KeywordsPROTEIN BINDING / PROTEASE INHIBITOR / IMMUNE EVASION
Function / homology
Function and homology information


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / purinergic nucleotide receptor signaling pathway / caspase binding / response to yeast / negative regulation of T cell activation / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / Activation of Matrix Metalloproteinases / cytokine binding / positive regulation of MAP kinase activity / monocyte chemotaxis / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / defense response to fungus / Purinergic signaling in leishmaniasis infection / response to UV / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / serine-type peptidase activity / positive regulation of smooth muscle cell proliferation / secretory granule / Regulation of Complement cascade / protein maturation / positive regulation of interleukin-8 production / protein catabolic process / positive regulation of immune response / protein processing / platelet activation / negative regulation of inflammatory response / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / intracellular calcium ion homeostasis / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / transcription corepressor activity / peptidase activity / heparin binding / : / cellular response to lipopolysaccharide / protease binding / response to lipopolysaccharide / endopeptidase activity / defense response to Gram-negative bacterium / lysosome / protein phosphorylation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / receptor ligand activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. ...MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Neutrophil elastase / Cathepsin G / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMishra, N.B. / Herdendorf, T.J. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.
Authors: Mishra, N. / Gido, C.D. / Herdendorf, T.J. / Hammel, M. / Hura, G.L. / Fu, Z.Q. / Geisbrecht, B.V.
History
DepositionFeb 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin-G
B: Neutrophil elastase
C: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6926
Polymers60,1673
Non-polymers1,5243
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint13 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.970, 110.389, 116.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Cathepsin-G


Mass: 25397.131 Da / Num. of mol.: 1 / Fragment: C-terminal truncation (UNP residues 21-243) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Neutrophil / References: UniProt: P08311
#2: Protein Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


Mass: 23318.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Neutrophil / References: UniProt: P08246, leukocyte elastase
#3: Protein Extracellular Adherence Protein / Protein map


Mass: 11451.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: map, SAV1938 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1

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Sugars , 3 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 205 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate 0.1 M imidazole (pH 6.8) 22% (w/v) peg-2kMME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 41637 / % possible obs: 99.5 % / Redundancy: 10.4 % / CC1/2: 0.965 / CC star: 0.991 / Rmerge(I) obs: 0.348 / Rpim(I) all: 0.111 / Rrim(I) all: 0.366 / Χ2: 0.994 / Net I/σ(I): 10.2 / Num. measured all: 433069
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.95-2.026.51.86240330.4420.7830.7392.010.89298.9
2.02-2.18.91.39841420.7430.9230.4821.480.94799.9
2.1-2.210.11.25541200.8420.9560.4021.3190.99499.8
2.2-2.3110.81.0541290.8830.9690.3241.10.99499.9
2.31-2.4611.10.78740970.920.9790.240.8231.01399.6
2.46-2.6511.10.5641080.9440.9860.1710.5861.00499.2
2.65-2.91100.35841550.9550.9880.1160.3771.02499.2
2.91-3.3312.20.23941910.9740.9930.070.251.024100
3.33-4.212.10.18342440.9820.9960.0550.1910.98100
4.2-5011.10.18444180.9410.9850.0580.1931.01498.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→40.14 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2005 4.82 %
Rwork0.1926 --
obs0.1944 41557 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 101 205 4519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074393
X-RAY DIFFRACTIONf_angle_d0.8515945
X-RAY DIFFRACTIONf_dihedral_angle_d13.8431662
X-RAY DIFFRACTIONf_chiral_restr0.059684
X-RAY DIFFRACTIONf_plane_restr0.008768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.32541170.2512530X-RAY DIFFRACTION89
2-2.060.27321530.21552762X-RAY DIFFRACTION99
2.06-2.120.24631390.20282815X-RAY DIFFRACTION100
2.12-2.190.22161440.1892813X-RAY DIFFRACTION100
2.19-2.270.22591350.19192806X-RAY DIFFRACTION100
2.27-2.360.25441400.19462827X-RAY DIFFRACTION100
2.36-2.460.23361460.19482816X-RAY DIFFRACTION100
2.46-2.590.21761480.19052826X-RAY DIFFRACTION99
2.59-2.760.2531340.20112833X-RAY DIFFRACTION100
2.76-2.970.25561490.20632829X-RAY DIFFRACTION99
2.97-3.270.24071440.20012855X-RAY DIFFRACTION100
3.27-3.740.18771510.17642892X-RAY DIFFRACTION100
3.74-4.710.21891470.16842923X-RAY DIFFRACTION100
4.71-40.140.21821580.20173025X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19940.13970.04790.10450.0261-0.00720.0739-0.3450.2350.13380.2352-0.1086-0.06060.35480.77330.0522-0.0405-0.26260.3223-0.34290.2327-32.457540.045343.6274
20.34230.0116-0.01420.54530.00740.34440.0233-0.36960.37250.20510.1320.38740.1139-0.07620.3078-0.09860.1640.03190.1839-0.0790.2349-45.664731.919541.2488
30.65950.2439-0.26760.8927-0.18190.5649-0.06590.10610.3726-0.17940.07380.1862-0.0137-0.1790.250.07860.0441-0.0380.1336-0.02020.2301-46.684132.45432.4055
40.69020.1953-0.50830.5-0.03940.4193-0.17310.42430.2656-0.1856-0.0847-0.0246-0.0949-0.1436-0.00780.0776-0.02550.02650.4111-0.07470.3626-28.101237.078226.1733
50.05280.0412-0.03780.4326-0.06210.5882-0.0518-0.35370.26620.05760.2135-0.32010.19020.29130.06240.14980.0303-0.02750.3363-0.09260.2505-26.879229.103239.6042
60.09510.0413-0.10360.1846-0.20390.2754-0.05450.4416-0.1217-0.13070.1097-0.120.0374-0.07710.01510.20880.0273-0.00770.2098-0.0320.1303-28.006320.835923.5048
70.2223-0.1231-0.23830.32890.02570.3113-0.0674-0.31550.47480.05250.1005-0.3024-0.11510.20140.03560.1044-0.0018-0.02060.1936-0.0310.2299-27.761328.784934.6546
80.1081-0.28870.02080.8527-0.08280.0269-0.0082-0.02360.2217-0.31540.038-0.155-0.2343-0.11850.17960.1750.057-0.0390.19080.05160.113-40.425932.088323.4096
90.0208-0.1117-0.0180.7310.15310.0287-0.1061-0.11230.00850.25680.07020.2621-0.0714-0.3737-0.06480.1776-0.0023-0.0510.26180.04480.2317-53.8351-13.255968.6394
100.1429-0.01670.00030.1256-0.02960.0351-0.068-0.03960.04710.0571-0.01760.0504-0.43540.01950.01160.29440.0216-0.04640.1002-0.00960.1373-39.2153-1.82969.0139
110.0126-0.0074-0.01770.00180.00560.0273-0.0098-0.2420.19790.1117-0.08940.34130.0307-0.3135-0.00040.44990.12370.04240.4021-0.02020.3489-54.2035-2.172175.5051
120.1922-0.08420.23370.2489-0.23980.35150.0032-0.00860.03230.0951-0.1095-0.1323-0.21380.138-0.00170.20730.0102-0.00680.14550.01770.1445-34.8364-7.214670.7433
130.034-0.1020.10850.346-0.36970.39460.22610.1246-0.3302-0.25060.0112-0.04910.72380.06870.25980.43810.0839-0.06880.1878-0.04820.2896-40.2536-23.320661.9799
140.13460.12580.12480.14990.0330.2445-0.04590.2481-0.0318-0.34230.03580.07070.1212-0.2410.00030.3441-0.0105-0.06570.24320.01310.2411-47.5884-12.983356.7851
150.1654-0.158-0.00970.2212-0.09280.1425-0.07980.1171-0.1677-0.10360.13270.19860.2926-0.19080.02460.2919-0.0282-0.06170.1441-0.00170.1643-45.3896-14.859859.1605
160.38360.226-0.19290.1476-0.18730.8207-0.18550.20080.0216-0.3313-0.0798-0.06690.23330.162-0.34760.34690.0519-0.07390.1787-0.00540.1612-36.1298-14.518260.0108
170.7741-0.08580.16740.3015-0.03510.2321-0.1956-0.31460.13110.13960.15090.0928-0.1073-0.1949-0.10620.1630.1230.02420.18630.06940.1907-40.048114.817746.7087
180.110.18170.10490.33670.13120.076-0.00470.0977-0.1391-0.04870.1625-0.03650.2125-0.16610.17370.18250.05530.00180.2220.07860.1846-42.401713.603947.3333
190.179-0.087-0.07690.03680.03270.03030.10720.17860.1389-0.06750.04580.03970.1055-0.42690.02080.3244-0.0355-0.04890.24550.07690.1579-43.5327.222541.888
200.0467-0.00550.00290.439-0.07740.0662-0.05660.0349-0.0593-0.04710.01430.05780.1252-0.0649-0.02490.7485-0.0820.01080.16660.09140.1898-40.65172.043932.2182
210.75140.4259-0.06030.4728-0.06491.0607-0.1357-0.0564-0.1452-0.4066-0.1635-0.42860.4040.0486-0.5820.27770.0409-0.01080.09690.07030.2086-32.47514.695346.9056
220.07830.0319-0.01920.0142-0.00810.003-0.08160.09620.0445-0.37550.10810.08290.0105-0.1732-0.01630.34810.0065-0.03210.13040.01440.1326-40.7683-1.757650.5034
230.1475-0.0275-0.08210.0830.02410.24270.1087-0.05380.0601-0.0371-0.0424-0.3451-0.12070.0836-0.01370.28130.00670.03440.07620.03720.2348-35.217611.017248.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 220 )
8X-RAY DIFFRACTION8chain 'A' and (resid 221 through 238 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 43 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 137 )
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 154 )
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 188 )
15X-RAY DIFFRACTION15chain 'B' and (resid 189 through 217 )
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 246 )
17X-RAY DIFFRACTION17chain 'C' and (resid 266 through 275 )
18X-RAY DIFFRACTION18chain 'C' and (resid 276 through 295 )
19X-RAY DIFFRACTION19chain 'C' and (resid 296 through 311 )
20X-RAY DIFFRACTION20chain 'C' and (resid 312 through 319 )
21X-RAY DIFFRACTION21chain 'C' and (resid 320 through 339 )
22X-RAY DIFFRACTION22chain 'C' and (resid 340 through 351 )
23X-RAY DIFFRACTION23chain 'C' and (resid 352 through 363 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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