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- PDB-7whu: Human Neutrophil Elastase in-complex with Ecotin Peptide -

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Basic information

Entry
Database: PDB / ID: 7whu
TitleHuman Neutrophil Elastase in-complex with Ecotin Peptide
Components
  • Ecotin Peptide
  • Neutrophil elastase
KeywordsIMMUNE SYSTEM / Inhibition / Elastase / Serine protease
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
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsShankar, S. / Jayaraman, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R154-000-C07-114 Singapore
CitationJournal: Protein Sci. / Year: 2022
Title: Sequence preference and scaffolding requirement for the inhibition of human neutrophil elastase by ecotin peptide
Authors: Bagga, T. / Loh, S.N. / Sivaraman, J. / Shankar, S.
History
DepositionDec 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
D: Neutrophil elastase
A: Neutrophil elastase
B: Neutrophil elastase
C: Neutrophil elastase
E: Ecotin Peptide
F: Ecotin Peptide
G: Ecotin Peptide
H: Ecotin Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83427
Polymers117,4248
Non-polymers5,41019
Water50428
1
D: Neutrophil elastase
H: Ecotin Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6446
Polymers29,3562
Non-polymers1,2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint3 kcal/mol
Surface area10260 Å2
MethodPISA
2
A: Neutrophil elastase
E: Ecotin Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4435
Polymers29,3562
Non-polymers1,0873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint3 kcal/mol
Surface area10420 Å2
MethodPISA
3
B: Neutrophil elastase
F: Ecotin Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9659
Polymers29,3562
Non-polymers1,6097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-8 kcal/mol
Surface area10840 Å2
MethodPISA
4
C: Neutrophil elastase
G: Ecotin Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7817
Polymers29,3562
Non-polymers1,4255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint2 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.242, 68.914, 130.851
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number3
Space group name H-MP121
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

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Protein / Protein/peptide , 2 types, 8 molecules DABCEFGH

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


Mass: 28549.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELANE, ELA2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P08246, leukocyte elastase
#2: Protein/peptide
Ecotin Peptide


Mass: 806.925 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Sugars , 5 types, 8 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.: 4
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
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 39 molecules

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


Mass: 92.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 297 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 3350 (PEG3350)

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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 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.89→47.45 Å / Num. obs: 22860 / % possible obs: 99.1 % / Redundancy: 10.7 % / Biso Wilson estimate: 38.5942829623 Å2 / Rsym value: 0.0125 / Net I/σ(I): 1.81
Reflection shellResolution: 2.89→2.91 Å / Num. unique obs: 2002 / Rsym value: 0.03

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNE

1hne


Resolution: 2.89→47.45 Å / Cross valid method: THROUGHOUT / σ(F): 37.94 / Phase error: 34.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3058 2011 8.8 %
Rwork0.2523 --
obs0.2703 22860 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6686 0 308 28 7022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077097
X-RAY DIFFRACTIONf_angle_d1.0339645
X-RAY DIFFRACTIONf_dihedral_angle_d12.4971150
X-RAY DIFFRACTIONf_chiral_restr0.0731176
X-RAY DIFFRACTIONf_plane_restr0.0071233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.33841290.35261333X-RAY DIFFRACTION82
2.97-3.050.35211400.34021489X-RAY DIFFRACTION91
3.05-3.130.34731400.32721468X-RAY DIFFRACTION91
3.14-3.240.27241440.31391504X-RAY DIFFRACTION91
3.24-3.350.29291450.28981497X-RAY DIFFRACTION91
3.35-3.490.34951420.28481469X-RAY DIFFRACTION91
3.49-3.640.351410.26781506X-RAY DIFFRACTION91
3.64-3.840.30961480.25621499X-RAY DIFFRACTION91
3.84-4.080.34751470.25961511X-RAY DIFFRACTION91
4.08-4.390.2651440.24331482X-RAY DIFFRACTION91
4.39-4.830.30931420.23081503X-RAY DIFFRACTION91
4.83-5.530.29951460.23321510X-RAY DIFFRACTION91
5.53-6.960.35021470.24651519X-RAY DIFFRACTION91
6.97-47.450.28311510.24251564X-RAY DIFFRACTION91

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