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- PDB-8d4u: Crystal Structure of Neutrophil Elastase Inhibited by Eap2 from S... -

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Basic information

Entry
Database: PDB / ID: 8d4u
TitleCrystal Structure of Neutrophil Elastase Inhibited by Eap2 from S. aureus
Components
  • Extracellular Adherence Protein
  • Neutrophil elastase
KeywordsHYDROLASE/INHIBITOR / PROTEIN BINDING / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus / HYDROLASE-INHIBITOR / PROTEIN BINDING complex
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / peptidase activity / heparin binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease ...MAP domain / MAP domain / MAP repeat profile. / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsGido, C.D. / 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)5R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family.
Authors: Gido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
History
DepositionJun 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil elastase
C: Extracellular Adherence Protein
B: Neutrophil elastase
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0477
Polymers68,6854
Non-polymers1,3623
Water6,161342
1
A: Neutrophil elastase
C: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4834
Polymers34,3422
Non-polymers1,1412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint14 kcal/mol
Surface area14020 Å2
MethodPISA
2
B: Neutrophil elastase
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5643
Polymers34,3422
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.507, 56.009, 86.041
Angle α, β, γ (deg.)90.000, 95.050, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


Mass: 23318.982 Da / Num. of mol.: 2 / Fragment: UNP residues 30-247 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Neutrophil / Plasmid details: Purified from human sputum / References: UniProt: P08246, leukocyte elastase
#2: Protein Extracellular Adherence Protein / Protein map


Mass: 11023.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: map, SAV1938 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1
#3: 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.: 2 / Source method: isolated from a natural 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
#4: 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: isolated from a natural source / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M Lithium Sulfate, 25%(w/v) PEG-3350

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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: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 56195 / % possible obs: 98.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.051 / Rrim(I) all: 0.132 / Χ2: 1.027 / Net I/σ(I): 9.8 / Num. measured all: 350923
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.974.11.09653460.8180.5091.2131.06894.1
1.97-2.0550.88855520.8690.3960.9751.0497.7
2.05-2.145.70.7756280.8890.3350.8421.06998.2
2.14-2.256.10.54954860.9460.2380.61.06897
2.25-2.397.10.36556800.9760.1470.3941.06699.5
2.39-2.5870.24856650.9850.10.2681.03899.6
2.58-2.846.80.15556990.9930.0630.1671.0199.7
2.84-3.256.40.09755840.9950.0410.1050.95497.5
3.25-4.097.30.06657600.9970.0260.0710.99899.8
4.09-506.80.05257950.9970.0220.0570.99698.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE, 1YN3

1hne

1yn3


Resolution: 1.9→37.98 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1871 3.55 %
Rwork0.1996 50770 -
obs0.2007 52641 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.08 Å2 / Biso mean: 46.7506 Å2 / Biso min: 13.84 Å2
Refinement stepCycle: final / Resolution: 1.9→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 90 342 5216
Biso mean--58.54 40.98 -
Num. residues----630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.30571040.28672989309371
1.95-2.010.30051250.26263419354481
2.01-2.070.30271330.24133594372785
2.07-2.150.26591400.23363753389388
2.15-2.230.2491400.22023747388789
2.23-2.330.22591520.21433984413694
2.33-2.460.24921500.20264062421296
2.46-2.610.27861520.20774105425797
2.61-2.810.2531530.21614175432899
2.81-3.10.22931500.2154131428197
3.1-3.540.22411550.19724228438398
3.54-4.460.22011570.166342464403100
4.46-37.980.17831600.17834337449798
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)
11.1936-0.34330.17640.660.05961.2046-0.0556-0.71560.10920.14230.0661-0.2805-0.11830.48810.11530.1404-0.0129-0.05590.4252-0.01010.2565-13.869718.05610.9326
21.7866-0.077-0.36831.0538-0.3921.5118-0.0062-0.7131-0.1820.17080.0071-0.16950.08760.3624-0.01190.15840.0318-0.07280.37090.04010.2395-17.357711.954411.5809
31.2679-0.3103-0.21881.8570.38621.7372-0.1051-0.5767-0.37340.2140.0907-0.01530.30960.2252-0.00460.15810.0417-0.04630.30170.09890.2526-23.17838.032312.5241
41.94431.2929-0.38291.5157-0.4050.58730.1866-0.15520.35730.19470.05490.0154-0.25170.131-0.0330.3015-0.06090.1059-0.0251-0.08820.4709-38.998737.497212.0264
52.50260.98190.31711.1174-0.85971.3835-0.1048-0.21720.8430.33410.0702-0.2236-0.0740.0874-0.12470.41360.41120.04480.7266-0.07230.7172-49.192738.02029.547
61.4451-0.86190.18185.8066-1.09432.55320.0989-0.45990.68550.5673-0.0917-0.0355-0.62630.11370.06860.4873-0.1674-0.00210.4752-0.11370.375-27.396135.499616.303
78.3662-4.7411-1.56137.3651.74133.10620.0806-0.51090.38650.61830.0540.3273-0.37460.2857-0.11860.3217-0.09090.08820.2512-0.10710.2656-38.92930.669119.2275
80.32811.4419-0.29326.3785-1.12042.14990.2429-0.3360.40480.4795-0.02480.4977-0.2971-0.0195-0.24520.4087-0.11520.15190.3351-0.04740.3704-48.625125.342721.8516
94.26052.806-4.62612.5125-2.8055.1322-0.12680.6228-0.1212-0.05210.21480.31280.3045-0.3644-0.09960.20240.0010.01950.1439-0.03140.2971-40.957426.04739.5687
103.90653.429-4.70473.9782-3.66055.98990.06290.0874-0.1617-0.3062-0.0643-0.06430.0321-0.05510.08290.25640.0241-0.00070.1719-0.03050.2616-32.959426.88795.0157
112.36910.30370.00382.3017-0.2761.99330.0412-0.4150.04560.151-0.03090.0140.00460.2926-0.08460.1786-0.0167-0.00750.2625-0.03160.194-32.092321.08714.4886
127.96360.934-1.40873.5585-1.04923.15280.14860.17210.467-0.09250.04370.2058-0.30980.3035-0.12730.2619-0.05030.04440.1559-0.08090.2568-36.462832.24669.5279
132.0670.2134-0.76431.0649-0.30043.41730.0452-0.58980.03441.0091-0.02820.45330.517-0.15250.06671.2019-0.16040.44560.67730.02440.3025-59.368910.876443.6119
141.3156-0.62061.55680.2972-0.66124.99680.44060.0162-0.13970.16260.01070.0660.87320.00950.23311.6332-0.33950.26920.94740.07320.3457-61.29692.361348.0258
150.6528-0.028-0.16880.3134-0.40080.59670.12390.0868-0.13440.6344-0.28910.9180.4587-1.2112-0.3690.8155-0.21450.41820.9013-0.03880.6603-67.620215.561434.4621
160.44580.3141-0.55840.2526-0.57432.25420.11240.0294-0.07410.6814-0.10130.38840.2825-0.7734-0.30331.142-0.20080.65450.9425-0.05430.6222-68.250414.054745.8813
170.74380.0714-0.35440.7446-0.39310.37590.3079-0.43820.2760.3341-0.0845-0.00320.00010.443-0.06311.44190.0020.28570.7965-0.04410.3488-51.970917.775744.1669
180.68960.6264-0.28532.30070.40894.38890.3604-0.65460.41191.1506-0.06370.1937-0.54150.6697-0.21940.9373-0.12250.21190.6094-0.08070.3217-52.092121.620538.2236
191.2052-0.62680.52130.59030.47034.03480.2242-0.3081-0.15670.7113-0.01960.24320.3636-0.2857-0.13050.5041-0.08840.03450.22830.06950.2832-55.8375-2.749217.1424
202.6417-0.2871-0.79833.73932.15485.98480.0514-0.4653-0.15080.41450.0730.06770.58930.1735-0.1640.3601-0.01310.02920.19610.06110.2367-48.00331.603418.2332
216.46380.9319-1.53083.4232-0.10853.21890.1373-0.03950.1930.3577-0.12670.3291-0.099-0.5422-0.01780.27820.00930.04320.24050.02410.2299-53.02198.411116.131
221.87930.8198-0.06011.90390.33632.78480.2203-0.3213-0.0080.6395-0.22850.42290.3423-0.45620.03370.4328-0.07310.09380.30890.02930.271-55.2756.426922.0929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 83 )A29 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 188 )A84 - 188
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 246 )A189 - 246
4X-RAY DIFFRACTION4chain 'C' and (resid 158 through 166 )C158 - 166
5X-RAY DIFFRACTION5chain 'C' and (resid 167 through 174 )C167 - 174
6X-RAY DIFFRACTION6chain 'C' and (resid 175 through 186 )C175 - 186
7X-RAY DIFFRACTION7chain 'C' and (resid 187 through 202 )C187 - 202
8X-RAY DIFFRACTION8chain 'C' and (resid 203 through 211 )C203 - 211
9X-RAY DIFFRACTION9chain 'C' and (resid 212 through 221 )C212 - 221
10X-RAY DIFFRACTION10chain 'C' and (resid 222 through 230 )C222 - 230
11X-RAY DIFFRACTION11chain 'C' and (resid 231 through 242 )C231 - 242
12X-RAY DIFFRACTION12chain 'C' and (resid 243 through 254 )C243 - 254
13X-RAY DIFFRACTION13chain 'B' and (resid 29 through 75 )B29 - 75
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 95 )B76 - 95
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 114 )B96 - 114
16X-RAY DIFFRACTION16chain 'B' and (resid 115 through 131 )B115 - 131
17X-RAY DIFFRACTION17chain 'B' and (resid 132 through 168 )B132 - 168
18X-RAY DIFFRACTION18chain 'B' and (resid 169 through 246 )B169 - 246
19X-RAY DIFFRACTION19chain 'D' and (resid 158 through 186 )D158 - 186
20X-RAY DIFFRACTION20chain 'D' and (resid 187 through 202 )D187 - 202
21X-RAY DIFFRACTION21chain 'D' and (resid 203 through 230 )D203 - 230
22X-RAY DIFFRACTION22chain 'D' and (resid 231 through 254 )D231 - 254

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