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- PDB-4wvp: Crystal structure of an activity-based probe HNE complex -

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Basic information

Entry
Database: PDB / ID: 4wvp
TitleCrystal structure of an activity-based probe HNE complex
Components
  • BTN-3V3-NLB-OMT-OIC-3V2
  • Neutrophil elastase
KeywordsHydrolase/Hydrolase Inhibitor / neutrophil elastase / acitivity-based probe / inhibitor / protease / complex / HNE / HyCoSuL / Hydrolase-Hydrolase 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 / 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 / Trypsin-like serine proteases ...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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
6-mer peptide BTN-PE5-NLB-OMT-OIC-AXY / Neutrophil elastase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsLechtenberg, B.C. / Kasperkiewicz, P. / Robinson, H.R. / Drag, M. / Riedl, S.J.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: The Elastase-PK101 Structure: Mechanism of an Ultrasensitive Activity-based Probe Revealed.
Authors: Lechtenberg, B.C. / Kasperkiewicz, P. / Robinson, H. / Drag, M. / Riedl, S.J.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Advisory
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Sep 9, 2015Group: Refinement description
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Neutrophil elastase
I: BTN-3V3-NLB-OMT-OIC-3V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,42913
Polymers24,4652
Non-polymers1,96411
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-2 kcal/mol
Surface area11040 Å2
2
E: Neutrophil elastase
I: BTN-3V3-NLB-OMT-OIC-3V2
hetero molecules

E: Neutrophil elastase
I: BTN-3V3-NLB-OMT-OIC-3V2
hetero molecules

E: Neutrophil elastase
I: BTN-3V3-NLB-OMT-OIC-3V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,28739
Polymers73,3966
Non-polymers5,89133
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
Buried area19880 Å2
ΔGint-81 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.120, 73.120, 69.451
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11I-201-

SO4

21I-201-

SO4

31I-308-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EI

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


Mass: 23318.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase
#2: Protein/peptide BTN-3V3-NLB-OMT-OIC-3V2


Type: Peptide-like / Class: Inhibitor / Mass: 1146.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: 6-mer peptide BTN-PE5-NLB-OMT-OIC-AXY

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Sugars , 2 types, 2 molecules

#3: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 1
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

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Non-polymers , 3 types, 211 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH8, 0.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.63→69.45 Å / Num. obs: 26261 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.031 / Net I/σ(I): 14.7 / Num. measured all: 280452 / Scaling rejects: 433
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.63-1.669.20.6263.11197112980.8560.216100
8.94-69.459.90.06428.517281740.9950.02199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.63 Å63.32 Å
Translation1.63 Å63.32 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPG
Resolution: 1.63→63.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1699 / WRfactor Rwork: 0.1376 / FOM work R set: 0.9049 / SU B: 2.605 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0807 / SU Rfree: 0.0806 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 1366 5.2 %RANDOM
Rwork0.1384 24873 --
obs0.14 26239 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 18.125 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å20 Å2
2---0.43 Å20 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 1.63→63.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 159 202 2025
Biso mean--33.12 27.93 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191887
X-RAY DIFFRACTIONr_bond_other_d0.0020.021833
X-RAY DIFFRACTIONr_angle_refined_deg1.8682.0482567
X-RAY DIFFRACTIONr_angle_other_deg1.24434150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94722.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42715259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7171520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_mcbond_it2.2180.681887
X-RAY DIFFRACTIONr_mcbond_other2.2160.681888
X-RAY DIFFRACTIONr_mcangle_it3.3481.0141105
LS refinement shellResolution: 1.633→1.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 108 -
Rwork0.206 1805 -
all-1913 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -51.874 Å / Origin y: 90.687 Å / Origin z: 0.824 Å
111213212223313233
T0.0537 Å2-0.0214 Å20.0011 Å2-0.0609 Å20.0007 Å2--0.0292 Å2
L0.5896 °20.0845 °2-0.085 °2-0.7727 °2-0.0041 °2--1.1116 °2
S-0.0224 Å °0.0187 Å °-0.0538 Å °-0.0403 Å °-0.0012 Å °-0.0272 Å °0.1068 Å °-0.0627 Å °0.0236 Å °

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