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- PDB-9fic: High-resolution X-ray structure of human PC1/3 (PCSK1) prodomain ... -

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Basic information

Entry
Database: PDB / ID: 9fic
TitleHigh-resolution X-ray structure of human PC1/3 (PCSK1) prodomain R77A,R80A,R81A triple-mutant
ComponentsNeuroendocrine convertase 1
KeywordsHYDROLASE / proprotein convertase subtilisin/kexin type 1 / PCSK1 / prodomain / activation
Function / homology
Function and homology information


proprotein convertase 1 / Peptide hormone biosynthesis / insulin processing / peptide biosynthetic process / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / peptide hormone processing / Insulin processing / Synthesis, secretion, and deacylation of Ghrelin / transport vesicle / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) ...proprotein convertase 1 / Peptide hormone biosynthesis / insulin processing / peptide biosynthetic process / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / peptide hormone processing / Insulin processing / Synthesis, secretion, and deacylation of Ghrelin / transport vesicle / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / cell-cell signaling / secretory granule lumen / neuron projection / serine-type endopeptidase activity / proteolysis / extracellular space / identical protein binding / 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 / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Neuroendocrine convertase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

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Assembly

Deposited unit
A: Neuroendocrine convertase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6214
Polymers9,5521
Non-polymers693
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-23 kcal/mol
Surface area4820 Å2
Unit cell
Length a, b, c (Å)60.010, 60.010, 40.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Neuroendocrine convertase 1 / NEC 1 / Prohormone convertase 1 / Proprotein convertase 1 / PC1


Mass: 9551.580 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20 % Polyethylene glycol 3,350

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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: 1.3→30 Å / Num. obs: 20558 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.999 / Net I/av σ(I): 13.92 / Net I/σ(I): 0.095
Reflection shellResolution: 1.3→1.38 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 3294 / CC1/2: 0.778 / Rrim(I) all: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSVERSION Jan 10, 2022data reduction
XDSVERSION Jan 10, 2022data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→30 Å / SU ML: 0.1258 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.3545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 1019 4.96 %
Rwork0.1404 19534 -
obs0.142 20553 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms614 0 3 95 712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071698
X-RAY DIFFRACTIONf_angle_d0.9058953
X-RAY DIFFRACTIONf_chiral_restr0.083193
X-RAY DIFFRACTIONf_plane_restr0.0067132
X-RAY DIFFRACTIONf_dihedral_angle_d14.0986256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.370.24141380.18572786X-RAY DIFFRACTION99.97
1.37-1.450.25131450.15982756X-RAY DIFFRACTION99.97
1.45-1.570.18981460.13712774X-RAY DIFFRACTION100
1.57-1.720.18971470.11542788X-RAY DIFFRACTION100
1.72-1.970.14831450.11062784X-RAY DIFFRACTION99.97
1.97-2.490.16211480.13622803X-RAY DIFFRACTION99.97
2.49-300.16321500.15152843X-RAY DIFFRACTION99.97

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