[English] 日本語
Yorodumi
- PDB-7cbk: Structure of Human Neutrophil Elastase Ecotin complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / cytokine binding / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / response to UV / phagocytosis / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / positive regulation of MAP kinase activity / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / serine-type endopeptidase inhibitor activity / protein catabolic process / defense response / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / transcription corepressor activity / azurophil granule lumen / peptidase activity / heparin binding / outer membrane-bounded periplasmic space / protease binding / : / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...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 / 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 / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more