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- PDB-7o20: X-ray structure of furin in complex with the guanylhydrazone-base... -

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Basic information

Entry
Database: PDB / ID: 7o20
TitleX-ray structure of furin in complex with the guanylhydrazone-based inhibitor 3 (mi300)
ComponentsFurin
KeywordsHYDROLASE / proprotein convertase / inhibitor / SARS-CoV-2 / protease / complex / furin
Function / homology
Function and homology information


furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / secretion by cell / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / nerve growth factor binding / Signaling by PDGF / trans-Golgi network transport vesicle / Elastic fibre formation / heparan sulfate binding / Signaling by NODAL / blastocyst formation / regulation of endopeptidase activity / peptide hormone processing / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / CD163 mediating an anti-inflammatory response / regulation of protein catabolic process / Activation of Matrix Metalloproteinases / Maturation of hRSV A proteins / TGF-beta receptor signaling activates SMADs / Respiratory syncytial virus (RSV) attachment and entry / Uptake and function of anthrax toxins / Collagen degradation / protein maturation / collagen catabolic process / extracellular matrix disassembly / regulation of signal transduction / Removal of aminoterminal propeptides from gamma-carboxylated proteins / viral life cycle / serine-type peptidase activity / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / negative regulation of inflammatory response to antigenic stimulus / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / serine-type endopeptidase inhibitor activity / protein processing / Golgi lumen / peptidase activity / heparin binding / protease binding / endopeptidase activity / viral translation / amyloid fibril formation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / viral protein processing / endosome membrane / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Furin-like repeat / Furin-like repeats / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Growth factor receptor cysteine-rich domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDahms, S.O. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundM 2730 Austria
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: OFF-State-Specific Inhibition of the Proprotein Convertase Furin.
Authors: Dahms, S.O. / Haider, T. / Klebe, G. / Steinmetzer, T. / Brandstetter, H.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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: Furin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53617
Polymers52,1121
Non-polymers1,42316
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-36 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.316, 130.316, 156.037
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Furin / Dibasic-processing enzyme / Paired basic amino acid residue-cleaving enzyme / PACE


Mass: 52112.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#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: obtained synthetically / 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 , 6 types, 385 molecules

#2: Chemical ChemComp-UYT / [azanyl-[(2E)-2-(1-phenylethylidene)hydrazinyl]methylidene]azanium / Diaminomethylidene-[(Z)-1-phenylethylideneamino]azanium / 7377553


Mass: 177.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→47.2 Å / Num. obs: 71888 / % possible obs: 98.5 % / Redundancy: 20 % / Biso Wilson estimate: 28.47 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.165 / Net I/σ(I): 16.29
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 11266 / CC1/2: 0.604 / Rrim(I) all: 2.763

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
XDSXDS VERSION Jan 31, 2020data reduction
XDSXDS VERSION Jan 31, 2020data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JXG

5jxg


Resolution: 1.8→45.72 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 3526 4.91 %
Rwork0.1624 68328 -
obs0.1631 71854 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 83 370 4011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933905
X-RAY DIFFRACTIONf_angle_d1.05485334
X-RAY DIFFRACTIONf_chiral_restr0.0627569
X-RAY DIFFRACTIONf_plane_restr0.0075715
X-RAY DIFFRACTIONf_dihedral_angle_d27.30161420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.29391530.29832578X-RAY DIFFRACTION95.66
1.82-1.850.30021380.2662668X-RAY DIFFRACTION97.53
1.85-1.880.28761360.25532666X-RAY DIFFRACTION97.63
1.88-1.90.24691460.23852668X-RAY DIFFRACTION97.71
1.9-1.940.25331310.22192692X-RAY DIFFRACTION98.02
1.94-1.970.24831250.20542674X-RAY DIFFRACTION97.97
1.97-20.2221300.19982703X-RAY DIFFRACTION97.89
2-2.040.20731350.1842679X-RAY DIFFRACTION98.25
2.04-2.090.16351500.17272681X-RAY DIFFRACTION98.09
2.09-2.130.18471410.16292697X-RAY DIFFRACTION98.27
2.13-2.180.18491450.15652690X-RAY DIFFRACTION98.3
2.18-2.230.17211430.14922716X-RAY DIFFRACTION98.42
2.23-2.30.1761180.1462716X-RAY DIFFRACTION98.4
2.3-2.360.17191320.14462745X-RAY DIFFRACTION98.59
2.36-2.440.17461300.14612713X-RAY DIFFRACTION98.65
2.44-2.530.17161330.13852734X-RAY DIFFRACTION98.83
2.53-2.630.16211290.14432756X-RAY DIFFRACTION98.9
2.63-2.750.15221510.14382744X-RAY DIFFRACTION98.87
2.75-2.890.19031440.14912763X-RAY DIFFRACTION99.01
2.89-3.070.16171490.15622750X-RAY DIFFRACTION99.25
3.07-3.310.16871510.1482768X-RAY DIFFRACTION99.32
3.31-3.640.15161520.15052806X-RAY DIFFRACTION99.33
3.64-4.170.1511500.14232814X-RAY DIFFRACTION99.46
4.17-5.250.1631540.14132867X-RAY DIFFRACTION99.54
5.25-45.720.19211600.20793040X-RAY DIFFRACTION99.38
Refinement TLS params.Method: refined / Origin x: 34.9952631104 Å / Origin y: -37.4216527858 Å / Origin z: 0.284887413297 Å
111213212223313233
T0.176044745382 Å2-0.00439348272401 Å2-0.00084269862319 Å2-0.221889813855 Å20.0156362732068 Å2--0.214298758491 Å2
L0.222156456504 °20.0331314774418 °2-0.0850291590503 °2-0.492381763297 °20.160931727257 °2--0.630667375718 °2
S0.00710397635675 Å °0.0114260580052 Å °0.00694465610647 Å °-0.0330600676817 Å °-0.0123248354055 Å °0.0558770722598 Å °-0.0191903301706 Å °-0.0763868319325 Å °-2.13917877859E-6 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection details: chain A / Auth asym-ID: A

IDLabel asym-IDAuth seq-IDLabel seq-ID
1A - Q110 - 5761
2601 - 616

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