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- PDB-9fie: X-ray structure of furin (PCSK3) in complex with the PC1/3 (PCSK1... -

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Basic information

Entry
Database: PDB / ID: 9fie
TitleX-ray structure of furin (PCSK3) in complex with the PC1/3 (PCSK1) prodomain mutant R77A,R80A,R81A
Components
  • Furin
  • Neuroendocrine convertase 1
KeywordsHYDROLASE / furin / proprotein convertase subtilisin/kexin type 3 / PCSK3 / PCSK1 / prodomain / complex / activation
Function / homology
Function and homology information


proprotein convertase 1 / Peptide hormone biosynthesis / insulin processing / furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes ...proprotein convertase 1 / Peptide hormone biosynthesis / insulin processing / furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / signal peptide processing / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / Pre-NOTCH Processing in Golgi / nerve growth factor binding / Synthesis and processing of ENV and VPU / cytokine precursor processing / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Formation of the cornified envelope / secretion by cell / Signaling by PDGF / trans-Golgi network transport vesicle / Signaling by NODAL / heparan sulfate binding / blastocyst formation / Elastic fibre formation / peptide hormone processing / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / CD163 mediating an anti-inflammatory response / Insulin processing / Activation of Matrix Metalloproteinases / Maturation of hRSV A proteins / regulation of protein catabolic process / TGF-beta receptor signaling activates SMADs / Collagen degradation / collagen catabolic process / Respiratory syncytial virus (RSV) attachment and entry / Uptake and function of anthrax toxins / extracellular matrix disassembly / Synthesis, secretion, and deacylation of Ghrelin / regulation of signal transduction / endopeptidase activator activity / Removal of aminoterminal propeptides from gamma-carboxylated proteins / transport vesicle / viral life cycle / extracellular matrix organization / serine-type peptidase activity / peptide binding / transforming growth factor beta receptor signaling pathway / protein maturation / negative regulation of inflammatory response to antigenic stimulus / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / protein processing / Golgi lumen / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / cell-cell signaling / peptidase activity / heparin binding / protease binding / secretory granule lumen / 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 / neuron projection / endosome membrane / viral protein processing / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Prohormone convertase enzyme / Prohormone convertase enzyme / 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 ...Prohormone convertase enzyme / Prohormone convertase enzyme / 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. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Furin / Neuroendocrine convertase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDahms, S.O. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP36648-B Austria
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into proprotein convertase activation facilitate the engineering of highly specific furin inhibitors.
Authors: Klaushofer, R. / Bloch, K. / Eder, L.S. / Marzaro, S. / Schubert, M. / Bottcher-Friebertshauser, E. / Brandstetter, H. / Dahms, S.O.
History
DepositionMay 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin
B: Neuroendocrine convertase 1
C: Furin
D: Neuroendocrine convertase 1
E: Furin
F: Neuroendocrine convertase 1
G: Furin
H: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,62428
Polymers247,7618
Non-polymers86320
Water15,691871
1
A: Furin
B: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1067
Polymers61,9402
Non-polymers1665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-53 kcal/mol
Surface area20380 Å2
MethodPISA
2
C: Furin
D: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0836
Polymers61,9402
Non-polymers1434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-42 kcal/mol
Surface area20690 Å2
MethodPISA
3
E: Furin
F: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3288
Polymers61,9402
Non-polymers3876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-50 kcal/mol
Surface area20490 Å2
MethodPISA
4
G: Furin
H: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1067
Polymers61,9402
Non-polymers1665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-51 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.800, 83.740, 103.160
Angle α, β, γ (deg.)98.500, 89.930, 95.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 52388.602 Da / Num. of mol.: 4
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
#2: Protein
Neuroendocrine convertase 1 / NEC 1 / Prohormone convertase 1 / Proprotein convertase 1 / PC1


Mass: 9551.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK1, NEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29120, proprotein convertase 1

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Sugars , 1 types, 1 molecules

#5: 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 / Feature type: SUBJECT OF INVESTIGATION
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 , 3 types, 890 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 3.75 M NaAc pH 7.0, 10 mM Hepes pH 7.4, 1 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 2→46.6 Å / Num. obs: 183598 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.989 / Rrim(I) all: 0.21 / Net I/σ(I): 5.52
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.17 / Num. unique obs: 13581 / CC1/2: 0.578 / Rrim(I) all: 1.261 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSVERSION Feb 5, 2021data reduction
XSCALEVERSION Feb 5, 2021data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.6 Å / SU ML: 0.2338 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.8888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 9177 5 %
Rwork0.1956 174368 -
obs0.1967 183545 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16890 0 33 871 17794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002717777
X-RAY DIFFRACTIONf_angle_d0.583424269
X-RAY DIFFRACTIONf_chiral_restr0.04412600
X-RAY DIFFRACTIONf_plane_restr0.00513255
X-RAY DIFFRACTIONf_dihedral_angle_d12.84476385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.34323040.31895772X-RAY DIFFRACTION98.89
2.02-2.050.33953060.3085829X-RAY DIFFRACTION99.9
2.05-2.070.31893080.28715837X-RAY DIFFRACTION99.82
2.07-2.10.30153070.27845845X-RAY DIFFRACTION99.84
2.1-2.130.30983040.27655786X-RAY DIFFRACTION99.89
2.13-2.150.29683070.26965841X-RAY DIFFRACTION99.87
2.15-2.190.2843070.25825824X-RAY DIFFRACTION99.85
2.19-2.220.26813050.24685790X-RAY DIFFRACTION99.85
2.22-2.250.29463070.24855834X-RAY DIFFRACTION99.68
2.25-2.290.27553070.24055828X-RAY DIFFRACTION99.45
2.29-2.330.26493050.23595799X-RAY DIFFRACTION99.38
2.33-2.370.25353050.22515786X-RAY DIFFRACTION99.35
2.37-2.420.25973040.21685785X-RAY DIFFRACTION99.67
2.42-2.470.25623070.2235842X-RAY DIFFRACTION99.93
2.47-2.520.23513060.21625847X-RAY DIFFRACTION99.87
2.52-2.580.25033070.21015819X-RAY DIFFRACTION99.82
2.58-2.640.25173060.2175823X-RAY DIFFRACTION99.85
2.64-2.710.24583050.21425791X-RAY DIFFRACTION99.74
2.71-2.790.23043070.21295823X-RAY DIFFRACTION99.84
2.79-2.880.25773080.22535858X-RAY DIFFRACTION99.76
2.88-2.990.24843050.21375800X-RAY DIFFRACTION99.69
2.99-3.110.21863060.20935812X-RAY DIFFRACTION99.77
3.11-3.250.21143070.19835814X-RAY DIFFRACTION99.76
3.25-3.420.20333040.18915779X-RAY DIFFRACTION99.23
3.42-3.630.18073050.16025800X-RAY DIFFRACTION99.41
3.63-3.910.17163060.14925822X-RAY DIFFRACTION99.8
3.91-4.310.14963070.12815819X-RAY DIFFRACTION99.76
4.31-4.930.13613070.12625829X-RAY DIFFRACTION99.58
4.93-6.210.1823040.1545776X-RAY DIFFRACTION99.41
6.21-46.60.18923040.18035758X-RAY DIFFRACTION98.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.852063950835-0.0801185583909-0.1472304620960.3578788671180.02948837322270.352214452174-0.004763984092710.08024670792130.1194967689460.00524600400942-0.00635604706289-0.01484744975960.03832645764090.0374827842674-7.61792967467E-70.2063939191950.0289366183893-0.0002164816285610.2417509678620.0103209342470.212244640557-17.1382500843-38.497386384430.7198373192
20.1969651698220.028233515516-0.03857940313560.07269358378930.02743234794930.0220985272891-0.153452215651-0.218880804937-0.02637217440730.09698824796330.1233164564740.0413844634479-0.03987196301020.00895811534338-2.89011776001E-50.2146378721140.05208291204010.01055435944850.3156427266520.01312050100810.3396200862719.32765714294-50.594407597830.4287878164
30.2230665211770.0430019963959-0.1018383695610.254047641529-0.06023872049710.490584348164-0.0119162421749-0.04806454403320.01324657296810.02824752214480.0207500003851-0.0212184395125-0.05798847943350.00839731664496-9.32580881091E-70.2041876790350.0262210135561-0.006758509410090.332600048858-0.008031440673950.19720247165214.9245472618-42.4751937651-19.5580575459
40.01539787998440.01090560758070.0787853954250.2840537299830.2018911657830.4931307316930.006623966574860.04158327046210.3541630030710.161969892757-0.08141604437420.340372837149-0.0287364047501-0.21261927207-0.01525797115610.2483012240140.0721739023112-0.02754046637240.294407261325-0.04042017956780.568356895983-0.442839878693-18.3129140148-10.9492806493
50.4787653091860.07168534413740.07002900144640.3827152799230.02194657002640.655126535545-0.0085981484002-0.00388731148248-0.0167959961053-0.0175032616946-0.0432117947172-0.004558413385590.0006762142765950.0155738429718-5.41576502749E-60.2237688204340.0367013084985-0.003821392452760.3016704739-0.01605284878590.198802924527-12.3458236512-72.471563233-26.7117382268
60.150075786945-0.0303356630560.03882659890820.0421807492969-0.01914307251820.0219239405059-0.102612517921-0.0831498588785-0.03232184303640.04440609748430.1004863360710.02762738440340.05429745597790.0534007732886-2.49434436354E-50.2153533660280.0683529262072-0.01702278136120.431558202568-0.06243855469050.311309126737-39.4208364758-60.7236768022-22.9697094074
70.4559550498840.05338640384570.09399343142380.263927344229-0.02181703389190.457087830163-0.006321825044980.00151693699241-0.0488455684082-0.01000035316190.01124898025730.03609081987970.0227357897587-0.03268566542163.4641868556E-60.1928221173890.0110394863412-0.002235443855650.242524852093-8.4332871521E-50.205236993174-44.4372404465-69.225924421328.4112769297
80.0513493447504-0.03254955779020.04248963146820.171708376911-0.03637102175060.05601313323990.1107006136460.09723710354430.00578424656758-0.127410376524-0.134943020868-0.07297366119680.04576648155660.0899746614847-2.06586165071E-50.2954930805640.02274156756250.005531358588260.2827568428560.01401709913770.451123071558-29.4363128541-95.203259265628.6991862278
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA110 - 5741 - 465
22chain BBH29 - 1101 - 82
33chain CCI108 - 5741 - 467
44chain DDO29 - 1101 - 82
55chain EEP - K110 - 5741
66chain FFW29 - 1101 - 82
77chain GGX108 - 5741 - 467
88chain HHH29 - 1101 - 82

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