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- PDB-7cbk: Structure of Human Neutrophil Elastase Ecotin complex -

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Basic information

Entry
Database: PDB / ID: 7cbk
TitleStructure of Human Neutrophil Elastase Ecotin complex
Components
  • Ecotin
  • Neutrophil elastase
KeywordsLYASE / Protease-inhibitor 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 / serine-type endopeptidase inhibitor activity / protein catabolic process / negative regulation of inflammatory response / defense response / specific granule lumen / intracellular calcium ion homeostasis / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / heparin binding / peptidase activity / outer membrane-bounded periplasmic space / 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 / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / 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. ...Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / 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 / Ecotin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis for the Inhibition Mechanism of Ecotin against Neutrophil Elastase by Targeting the Active Site and Secondary Binding Site.
Authors: Jobichen, C. / Prabhakar, M.T. / Loh, S.N. / Sivaraman, J.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ecotin
C: Ecotin
D: Neutrophil elastase
B: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,76812
Polymers93,5264
Non-polymers2,2418
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-32 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.192, 165.102, 63.998
Angle α, β, γ (deg.)90.000, 108.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 88 or resid 91 through 130 or resid 132 or resid 135 through 142))
21(chain C and (resid 11 through 76 or (resid 77...
12(chain B and (resid 16 through 62B or (resid 63...
22(chain D and (resid 16 through 243 or resid 406 through 411))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 11 through 88 or resid 91 through 130 or resid 132 or resid 135 through 142))A11 - 88
121(chain A and (resid 11 through 88 or resid 91 through 130 or resid 132 or resid 135 through 142))A91 - 130
131(chain A and (resid 11 through 88 or resid 91 through 130 or resid 132 or resid 135 through 142))A132
141(chain A and (resid 11 through 88 or resid 91 through 130 or resid 132 or resid 135 through 142))A135 - 142
211(chain C and (resid 11 through 76 or (resid 77...C11 - 76
221(chain C and (resid 11 through 76 or (resid 77...C77
231(chain C and (resid 11 through 76 or (resid 77...C10 - 142
241(chain C and (resid 11 through 76 or (resid 77...C10 - 142
251(chain C and (resid 11 through 76 or (resid 77...C10 - 142
261(chain C and (resid 11 through 76 or (resid 77...C10 - 142
112(chain B and (resid 16 through 62B or (resid 63...B16 - 62
122(chain B and (resid 16 through 62B or (resid 63...B63 - 64
132(chain B and (resid 16 through 62B or (resid 63...B16 - 511
142(chain B and (resid 16 through 62B or (resid 63...B16 - 511
152(chain B and (resid 16 through 62B or (resid 63...B16 - 511
162(chain B and (resid 16 through 62B or (resid 63...B16 - 511
212(chain D and (resid 16 through 243 or resid 406 through 411))D16 - 243
222(chain D and (resid 16 through 243 or resid 406 through 411))D406 - 411

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACDB

#1: Protein Ecotin


Mass: 18214.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: eco, eti, b2209, JW2197
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P23827
#2: Protein Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


Mass: 28549.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase

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Sugars , 2 types, 4 molecules

#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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 genetically manipulated 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

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Non-polymers , 4 types, 183 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5 and 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 23724 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rsym value: 0.104 / Net I/σ(I): 17.7
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 1127 / Rsym value: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE, 1ECZ

1hne

1ecz


Resolution: 2.7→24.426 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 1864 8.39 %
Rwork0.1991 20363 -
obs0.2047 22227 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.62 Å2 / Biso mean: 39.9462 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 2.7→24.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 145 179 5656
Biso mean--64.63 30.03 -
Num. residues----700
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A748X-RAY DIFFRACTION6.205TORSIONAL
12C748X-RAY DIFFRACTION6.205TORSIONAL
21B1388X-RAY DIFFRACTION6.205TORSIONAL
22D1388X-RAY DIFFRACTION6.205TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7002-2.77310.32321280.2645145690
2.7731-2.85460.36681300.2628149391
2.8546-2.94660.30861390.2659145990
2.9466-3.05170.30291440.2461154393
3.0517-3.17370.29181420.2454153095
3.1737-3.31780.29581460.2387160697
3.3178-3.49220.30031440.2132156797
3.4922-3.71030.2921470.2013160198
3.7103-3.99570.28881420.1785162898
3.9957-4.39570.21061470.1631157397
4.3957-5.02690.18871440.157163199
5.0269-6.31520.23571550.1745162799
6.3152-24.4260.24951560.17431649100
Refinement TLS params.Method: refined / Origin x: 20.3285 Å / Origin y: 110.5259 Å / Origin z: 44.135 Å
111213212223313233
T0.2105 Å20.0013 Å2-0.0021 Å2-0.2679 Å20.0036 Å2--0.2167 Å2
L0.0112 °2-0.1521 °20.053 °2-1.6262 °2-0.2463 °2--0.0275 °2
S0.0027 Å °0.0422 Å °-0.0021 Å °-0.0663 Å °0.0144 Å °-0.0427 Å °0.0274 Å °0.0382 Å °-0.0102 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 142
2X-RAY DIFFRACTION1allC10 - 142
3X-RAY DIFFRACTION1allD16 - 243
4X-RAY DIFFRACTION1allD406 - 501
5X-RAY DIFFRACTION1allB16 - 511
6X-RAY DIFFRACTION1allE1 - 2
7X-RAY DIFFRACTION1allS1 - 195
8X-RAY DIFFRACTION1allF1

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