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

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Basic information

Entry
Database: PDB / ID: 9fid
TitleX-ray structure of furin (PCSK3) in complex with the PC1/3 (PCSK1) prodomain mutant R78K,R80A
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: 2.4 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
D: Neuroendocrine convertase 1
B: Furin
E: Neuroendocrine convertase 1
C: Furin
F: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,68315
Polymers190,3746
Non-polymers3099
Water1,910106
1
A: Furin
D: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5615
Polymers63,4582
Non-polymers1033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Furin
E: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5615
Polymers63,4582
Non-polymers1033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Furin
F: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5615
Polymers63,4582
Non-polymers1033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.480, 196.980, 99.870
Angle α, β, γ (deg.)90.000, 106.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 110 through 124 or resid 130 through 574 or resid 600 through 602))
d_2ens_1(chain "B" and (resid 110 through 124 or resid 130 through 574 or resid 600 through 602))
d_3ens_1chain "C"
d_1ens_2(chain "D" and (resid 30 through 72 or resid 84 through 110))
d_2ens_2chain "E"
d_3ens_2(chain "F" and (resid 30 through 72 or resid 84 through 110))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1TYRTYRLEULEUAA110 - 1243 - 17
d_12ens_1ARGARGALAALAAA130 - 57423 - 467
d_13ens_1CACACACAAG600
d_14ens_1CACACACAAH601
d_21ens_1TYRTYRLEULEUBC110 - 1243 - 17
d_22ens_1ARGARGALAALABC130 - 57423 - 467
d_23ens_1CACACACABJ600
d_24ens_1CACACACABK601
d_31ens_1TYRTYRALAALACE110 - 5743 - 467
d_32ens_1CACACACACM600
d_33ens_1CACACACACN601
d_11ens_2GLNGLNHISHISDB30 - 7215 - 57
d_12ens_2PHEPHEARGARGDB84 - 11069 - 95
d_21ens_2GLNGLNARGARGED30 - 11015 - 95
d_31ens_2GLNGLNHISHISFF30 - 7215 - 57
d_32ens_2PHEPHEARGARGFF84 - 11069 - 95

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.64828286462, 0.205531073354, 0.733134575182), (0.215193071106, -0.874161599098, 0.435354385313), (0.730356946697, 0.439998268803, 0.522475122721)-28.9342385437, -20.213052922, 19.821181878
2given(-0.342551069373, 0.708802292451, 0.616650691306), (0.686823584393, -0.258918002224, 0.679142718467), (0.641039880814, 0.656171302588, -0.398129492585)-23.3576682801, 24.8407542894, -3.24319838968
3given(-0.660776778874, 0.220514228139, 0.717459074574), (0.209994131723, -0.863384943744, 0.458768899947), (0.720608432606, 0.453806031367, 0.524198028185)-28.9613052118, -21.0238736069, 19.6150644343
4given(-0.339131871527, 0.731301798004, 0.591766215621), (0.677214936914, -0.246840072705, 0.693144939914), (0.652969756524, 0.635820461092, -0.411537165176)-23.0282380746, 24.1429349717, -2.36330709383

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Components

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


Mass: 52388.602 Da / Num. of mol.: 3
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: 11069.346 Da / Num. of mol.: 3
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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 100 mM NaCitrate, pH 5.9, 500 mM (NH4)2SO4, 0.8-1.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.4→49.2 Å / Num. obs: 63282 / % possible obs: 75.1 % / Redundancy: 20.4 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.933 / Rrim(I) all: 0.53 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.28 / Num. unique obs: 4868 / CC1/2: 0.239 / Rrim(I) all: 2.477 / % possible all: 78.3

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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: 2.4→43.78 Å / SU ML: 0.3294 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2515 3073 4.86 %
Rwork0.2267 60188 -
obs0.2279 63261 75.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.79 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12337 0 9 106 12452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002512620
X-RAY DIFFRACTIONf_angle_d0.589117172
X-RAY DIFFRACTIONf_chiral_restr0.04431852
X-RAY DIFFRACTIONf_plane_restr0.00392279
X-RAY DIFFRACTIONf_dihedral_angle_d12.44194491
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.434338761135
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.480147008255
ens_2d_2BDX-RAY DIFFRACTIONTorsion NCS0.507643022156
ens_2d_3BDX-RAY DIFFRACTIONTorsion NCS0.665868402597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.31351440.29962897X-RAY DIFFRACTION78.8
2.44-2.480.33211490.29412746X-RAY DIFFRACTION77.34
2.48-2.520.29761520.2912809X-RAY DIFFRACTION77.82
2.52-2.570.31811640.2782868X-RAY DIFFRACTION78.2
2.57-2.620.33391370.28962767X-RAY DIFFRACTION77.34
2.62-2.670.32841490.28512822X-RAY DIFFRACTION77.17
2.67-2.730.34091260.28882815X-RAY DIFFRACTION77.33
2.73-2.790.27481410.28482805X-RAY DIFFRACTION77.26
2.79-2.860.36111390.28582804X-RAY DIFFRACTION76.44
2.86-2.940.30491530.25992798X-RAY DIFFRACTION76.97
2.94-3.020.3081440.26672724X-RAY DIFFRACTION75.37
3.02-3.120.29511470.24982730X-RAY DIFFRACTION75.41
3.12-3.230.24381460.24682754X-RAY DIFFRACTION75.7
3.23-3.360.25961320.24552723X-RAY DIFFRACTION75.33
3.36-3.520.251440.21282714X-RAY DIFFRACTION74.62
3.52-3.70.23011250.20472759X-RAY DIFFRACTION75.08
3.7-3.930.19371330.19242711X-RAY DIFFRACTION74.29
3.93-4.240.19061460.17022669X-RAY DIFFRACTION73.73
4.24-4.660.19991460.16472618X-RAY DIFFRACTION72.43
4.66-5.330.18861110.17582668X-RAY DIFFRACTION71.88
5.33-6.720.22511280.20352606X-RAY DIFFRACTION71.07
6.72-43.780.22271170.21582381X-RAY DIFFRACTION64.38
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)
10.383757332302-0.0788958462141-0.0794030050450.2866416466720.04186188849360.2585074054590.001591837563240.0296617795301-0.001239439240510.0376192681593-0.00352064908121-0.02700684560630.0189632943368-0.000905424194879-1.30197837088E-60.232419147224-0.00211870980437-0.00308167976150.2379820276320.01177403476060.261317460003-4.716870300121.852762967730.2265661154
20.411513928248-0.1298096215550.07690855874130.315307160051-0.04497999784720.07121132783060.01206173493420.0135544273873-0.003325073586910.0382960510531-0.00295672545986-0.02469782253280.0185784508162-0.01206593000422.49546295851E-60.27344504847-0.0117958508364-0.01389883714650.250531235681-0.02510705012030.2664086846530.692962142914-27.179498997141.9616931109
30.2874440642770.1086677502220.06715226849110.223732530414-0.02172912343770.294212546983-0.00513458370949-0.00351894406364-0.00573894478993-0.0239437820285-0.01085019913220.00844221481686-0.004274594530060.04315739403732.31786722886E-70.2341621746360.00116418369368-0.0004788574297770.2367547464780.01499076494250.2020387651212.395172838636.4387007453-3.98786711166
40.0401380223951-0.0267890943522-0.01851563021080.07276655579050.09270791728350.1530649422320.123346282121-0.09003795991080.0474740576779-0.0877702545072-0.120264549186-0.2924403988970.01951378482840.1522286565740.001007742960540.2957440224570.0130445317801-0.02452896649850.2920936934660.02591864846810.266680149974-23.95886986030.8089927896823.2042246071
50.193418215453-0.08443666616230.0776317956810.07841969441830.005617274924770.0682748882606-0.0343304141835-0.0922228972491-0.0875164708556-0.03688448024170.150530978392-0.04624186400340.188390078920.05958906711420.0180174064620.369452350334-0.03451525699020.04597661640050.324899821241-0.0829266783340.3605238169053.73153172622-16.044767673214.9477943961
60.14979718122-0.03858900811030.0106919008230.107310679647-0.03527214404120.0204133755303-0.00792097755549-0.0724905575055-0.0015206014617-0.0945788989571-0.0419681417478-0.07522427827180.391590455295-0.0729786189636-0.006853848288920.419608007724-0.02592028570090.02313020460370.342192164410.02669348838980.215242180548-0.60213814465823.6719679002-26.9744194672
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA110 - 5741 - 461
22chain BBG110 - 5741 - 465
33chain CCM110 - 5741 - 460
44chain DDF30 - 1101 - 71
55chain EEL30 - 1101 - 70
66chain FFR30 - 1101 - 72

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