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- PDB-8d4q: Crystal Structure of Neutrophil Elastase Inhibited by Eap1 from S... -

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Basic information

Entry
Database: PDB / ID: 8d4q
TitleCrystal Structure of Neutrophil Elastase Inhibited by Eap1 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 / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / negative regulation of interleukin-8 production / leukocyte migration involved in inflammatory response / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / negative regulation of interleukin-8 production / leukocyte migration involved in inflammatory response / negative regulation of chemokine production / Antimicrobial peptides / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / cytokine binding / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / Pyroptosis / extracellular matrix disassembly / phagocytosis / phagocytic vesicle / response to UV / transcription repressor complex / 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 / specific granule lumen / intracellular calcium ion homeostasis / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / heparin binding / peptidase activity / protease binding / collagen-containing extracellular matrix / endopeptidase activity / 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 / cytosol / cytoplasm
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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Neutrophil elastase
C: Extracellular Adherence Protein
B: Neutrophil elastase
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2918
Polymers69,0094
Non-polymers2,2824
Water4,017223
1
A: Neutrophil elastase
C: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6464
Polymers34,5052
Non-polymers1,1412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint17 kcal/mol
Surface area14430 Å2
MethodPISA
2
B: Neutrophil elastase
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6464
Polymers34,5052
Non-polymers1,1412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint20 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.646, 88.477, 89.436
Angle α, β, γ (deg.)90.000, 123.130, 90.000
Int Tables number5
Space group name H-MC121

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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 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Purified from human sputum / References: UniProt: P08246, leukocyte elastase
#2: Protein Extracellular Adherence Protein / Protein map


Mass: 11185.606 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.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 0.1M sodium citrate (pH 5.2), 12% (w/v) PEG-6000

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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: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42731 / % possible obs: 96.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 34.09 Å2 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.064 / Rrim(I) all: 0.164 / Χ2: 1.014 / Net I/σ(I): 11.4 / Num. measured all: 258666
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.50.62537420.6350.3010.6991.0784.6
2.28-2.374.50.48539630.8630.240.5451.02389.1
2.37-2.485.10.47141840.8680.2230.5241.01195
2.48-2.615.90.46643710.9020.2110.5141.01398.6
2.61-2.776.50.51644310.9320.2160.5611.02599.5
2.77-2.996.80.34443920.9560.1420.3731.02699.3
2.99-3.296.50.23244140.7880.0980.2531.01599.5
3.29-3.766.50.14242990.9880.0590.1541.03296.8
3.76-4.7470.10144640.9920.0410.111.00999.8
4.74-506.70.07744710.9930.0320.0830.95198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE, 8D4O

1hne

8d4o


Resolution: 2.2→38.09 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1858 4.67 %
Rwork0.1809 37967 -
obs0.1826 39825 88.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.87 Å2 / Biso mean: 48.5277 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.2→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 152 223 5211
Biso mean--70.4 45.78 -
Num. residues----634
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 (%)
2.2-2.260.3029980.29021976207460
2.26-2.320.32481150.26192466258175
2.32-2.40.29791310.24832487261877
2.4-2.480.28481340.23532776291085
2.48-2.580.27061350.23092870300588
2.58-2.70.25331460.22093019316592
2.7-2.840.25821480.22563074322294
2.84-3.020.25671550.2113106326195
3.02-3.260.2411580.19853199335797
3.26-3.580.21530.17833122327595
3.58-4.10.20221610.15333268342999
4.1-5.160.15791610.131633103471100
5.17-38.090.1891630.15963294345798
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)
10.25760.5781-0.66811.6603-1.95182.3709-0.0827-0.0709-0.26040.11960.24360.7810.3125-0.8202-0.12150.151-0.1740.2481.00020.54580.4763-24.165-32.53919.087
21.9890.52080.65052.2048-0.34861.7314-0.0646-0.0828-0.3913-0.41590.4230.25490.627-0.5952-0.25040.382-0.152-0.02420.35550.11020.3244-11.184-34.69910.01
33.94160.04140.85522.323-0.0944.0391-0.09480.022-0.0153-0.20150.21360.04950.0271-0.1102-0.16740.2032-0.01920.02820.18210.06170.1829-7.109-25.87810.927
42.49840.514-1.48282.2989-0.92894.89120.1861-0.68130.46171.00020.29060.6031-0.7167-0.949-0.48730.58150.18930.06240.54160.05150.3904-15.023-19.18827.096
53.92061.08921.27722.37790.94662.32720.2766-0.5795-0.22050.86750.21740.03590.3148-0.8046-0.30040.52420.00040.05570.57220.19990.2817-14.015-32.69528.209
62.1795-0.038-0.69992.9528-0.72212.9432-0.1418-0.7564-0.08140.51730.26580.2338-0.0231-0.4661-0.09530.27180.05170.02690.51070.0850.2307-10.461-26.73125.081
71.0292-0.8493-0.60991.5009-0.53642.92970.40760.0685-0.6563-0.1943-0.2216-0.02781.15120.0327-0.05920.72930.0787-0.01150.229-0.01250.40267.898-53.77821.324
86.86073.35097.42332.27982.6589.7002-0.25950.2018-0.1427-0.0435-0.6742-0.16061.1487-0.0791.04850.80270.00590.1210.85780.03810.781118.867-54.40428.059
93.3709-1.64980.08185.00690.55822.6703-0.03760.278-0.4121-0.54950.22640.54061.1082-0.2152-0.08630.6873-0.1267-0.0690.37980.00070.4123-1.334-51.98117.846
107.3468-3.20863.9819.3973-4.7248.5899-0.104-0.4661-0.56970.28650.66310.04181.0418-0.4421-0.58070.5828-0.0091-0.04680.29470.02190.3123.442-51.52230.162
111.39040.0873-2.20816.8934-0.25184.1661-0.2575-0.1098-0.2326-0.19580.31610.19690.19180.1659-0.10190.59210.0437-0.09050.32320.06110.35127.43-47.80740.772
120.774-0.46950.17950.5708-0.65422.90910.14730.1787-0.04440.15160.2212-0.2076-0.68790.5048-0.23180.49470.07240.02810.30850.01780.40379.014-42.46525.192
132.9079-0.8144-2.43821.43320.7212.09220.36920.16240.75160.0530.3528-0.061-0.3718-0.1539-0.60190.43660.05360.04480.27690.00340.3577.403-39.53919.875
142.5121-0.11541.64391.53350.23032.2757-0.0923-0.0541-0.3044-0.0950.45260.0471-0.2485-0.4359-0.39430.35330.03630.01740.34740.05670.2787-1.273-39.65426.73
153.995-0.27560.61772.7568-0.7036.753-0.42940.59940.5262-0.0494-0.0718-0.2327-0.16510.57130.55560.56140.034-0.00170.17150.02090.3948.471-46.69121.915
162.30620.04490.5172.1238-0.89642.7564-0.1655-0.23920.02790.28990.2060.2674-0.5821-0.5558-0.01660.310.13520.01510.34320.07250.278-0.008-50.42869.045
171.42090.85521.60192.0358-1.21774.90310.17960.155-0.4347-0.59550.04770.63530.5675-0.7138-0.17980.3494-0.0491-0.09530.39440.06560.4059-3.618-63.22554.232
182.79250.2202-0.98921.0512-0.00164.25820.10590.09770.0132-0.41240.02060.4894-0.7067-0.79-0.15370.39910.1421-0.07970.43390.10720.3509-7.562-50.19754.039
192.05360.2672-0.09183.0279-0.65792.7635-0.07540.08480.0547-0.22760.1670.2477-0.0835-0.4638-0.04990.23710.0344-0.0290.30830.0620.286-1.58-54.42655.491
201.82891.7341-0.29462.1155-1.60954.5238-0.16580.41550.36470.99050.04570.4394-1.0075-0.35870.04280.89680.0498-0.03690.27940.03190.4345.998-22.4757.189
211.96930.18881.63866.84076.04226.44030.241.01841.158-0.99171.4393-0.3974-0.7120.7965-1.43181.0783-0.29810.14030.82950.19780.849215.936-18.49946.863
220.96970.19350.06272.10750.77830.56830.1707-0.46370.89940.8702-0.00220.9197-0.63220.2275-0.17950.93390.07990.18220.3354-0.01750.5877-0.153-27.51861.466
232.6478-0.1899-0.10432.376-3.72026.1829-0.41430.17120.21990.09030.45940.3415-1.1096-0.5344-0.13890.6610.092-0.06340.2950.08850.48451.083-26.68548.621
242.6246-0.64041.09616.76276.6987.7856-0.38760.1070.43610.48050.0835-0.3911-0.89540.31160.28940.66350.0645-0.02110.34550.05340.36121.904-27.91637.935
251.7789-0.15512.75790.7851-0.80735.08660.23950.38880.0470.37620.1208-0.2437-0.12471.0563-0.08810.6388-0.0394-0.07040.31990.01810.362810.247-32.75847.353
263.61910.94472.88821.73091.0232.37110.24250.0707-0.67240.1462-0.3529-0.09470.37650.40570.00150.54790.0391-0.13010.3180.0080.39711.66-35.90256.885
271.11690.5388-1.10780.376-0.45672.00970.2783-0.070.09780.25820.27950.1477-0.3687-0.2813-0.49880.5320.0548-0.03450.27480.05260.3412.004-39.25552.452
281.77250.19310.56392.6315-0.20339.5982-0.1418-0.2901-0.15580.5389-0.1623-0.03090.09580.74670.38520.7897-0.0417-0.0650.2221-0.01770.42989.533-28.94454.954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:42 )A29 - 42
2X-RAY DIFFRACTION2( CHAIN A AND RESID 43:95 )A43 - 95
3X-RAY DIFFRACTION3( CHAIN A AND RESID 96:137 )A96 - 137
4X-RAY DIFFRACTION4( CHAIN A AND RESID 138:154 )A138 - 154
5X-RAY DIFFRACTION5( CHAIN A AND RESID 155:188 )A155 - 188
6X-RAY DIFFRACTION6( CHAIN A AND RESID 189:246 )A189 - 246
7X-RAY DIFFRACTION7( CHAIN C AND RESID 47:57 )C47 - 57
8X-RAY DIFFRACTION8( CHAIN C AND RESID 58:65 )C58 - 65
9X-RAY DIFFRACTION9( CHAIN C AND RESID 66:77 )C66 - 77
10X-RAY DIFFRACTION10( CHAIN C AND RESID 78:93 )C78 - 93
11X-RAY DIFFRACTION11( CHAIN C AND RESID 94:104 )C94 - 104
12X-RAY DIFFRACTION12( CHAIN C AND RESID 105:112 )C105 - 112
13X-RAY DIFFRACTION13( CHAIN C AND RESID 113:121 )C113 - 121
14X-RAY DIFFRACTION14( CHAIN C AND RESID 122:133 )C122 - 133
15X-RAY DIFFRACTION15( CHAIN C AND RESID 134:145 )C134 - 145
16X-RAY DIFFRACTION16( CHAIN B AND RESID 29:137 )B29 - 137
17X-RAY DIFFRACTION17( CHAIN B AND RESID 138:154 )B138 - 154
18X-RAY DIFFRACTION18( CHAIN B AND RESID 155:188 )B155 - 188
19X-RAY DIFFRACTION19( CHAIN B AND RESID 189:246 )B189 - 246
20X-RAY DIFFRACTION20( CHAIN D AND RESID 47:56 )D47 - 56
21X-RAY DIFFRACTION21( CHAIN D AND RESID 57:65 )D57 - 65
22X-RAY DIFFRACTION22( CHAIN D AND RESID 66:77 )D66 - 77
23X-RAY DIFFRACTION23( CHAIN D AND RESID 78:93 )D78 - 93
24X-RAY DIFFRACTION24( CHAIN D AND RESID 94:101 )D94 - 101
25X-RAY DIFFRACTION25( CHAIN D AND RESID 102:112 )D102 - 112
26X-RAY DIFFRACTION26( CHAIN D AND RESID 113:121 )D113 - 121
27X-RAY DIFFRACTION27( CHAIN D AND RESID 122:133 )D122 - 133
28X-RAY DIFFRACTION28( CHAIN D AND RESID 134:145 )D134 - 145

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