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- PDB-9szy: PCSK9 CTD fragment structure -

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Basic information

Entry
Database: PDB / ID: 9szy
TitlePCSK9 CTD fragment structure
Components(Proprotein convertase subtilisin/kexin type 9) x 2
KeywordsCHAPERONE / PCSK9 / CTD / fragment
Function / homology
Function and homology information


low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process ...low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / low-density lipoprotein particle binding / LDL clearance / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / transporter inhibitor activity / signaling receptor inhibitor activity / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / sodium channel inhibitor activity / endolysosome membrane / negative regulation of low-density lipoprotein particle clearance / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of receptor internalization / apolipoprotein binding / cholesterol metabolic process / phospholipid metabolic process / neurogenesis / regulation of neuron apoptotic process / cholesterol homeostasis / cellular response to starvation / VLDLR internalisation and degradation / Post-translational protein phosphorylation / kidney development / liver development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to insulin stimulus / neuron differentiation / late endosome / positive regulation of neuron apoptotic process / endopeptidase activity / early endosome / lysosome / endoplasmic reticulum lumen / serine-type endopeptidase activity / lysosomal membrane / apoptotic process / perinuclear region of cytoplasm / cell surface / Golgi apparatus / endoplasmic reticulum / : / RNA binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / : / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
: / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å
AuthorsJohansson, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Not funded Sweden
CitationJournal: Circulation / Year: 2026
Title: Laroprovstat, the First Oral Small-Molecule PCSK9 Inhibitor for the Treatment of Hypercholesterolemia: Results From a Randomized, Single-Blind, Placebo-Controlled Phase 1 Trial in Treatment-Naive Patients.
Authors: Vega, R.B. / O'Mahony, G. / Barbour, A.M. / Yu, H. / Knochel, J. / Brengdahl, J. / Hochdorfer, T. / Bergenholm, L. / Toppner Carlsson, E. / Ahnmark, A. / Underwood, C.R. / Rudvik, A. / ...Authors: Vega, R.B. / O'Mahony, G. / Barbour, A.M. / Yu, H. / Knochel, J. / Brengdahl, J. / Hochdorfer, T. / Bergenholm, L. / Toppner Carlsson, E. / Ahnmark, A. / Underwood, C.R. / Rudvik, A. / Carter, D. / Laru, J. / Gutgsell, A. / Twaddle, L. / Garkaviy, P. / Bogstedt, A. / Hurt-Camejo, E. / Miliotis, T. / Ryaboshapkina, M. / Hober, A. / Hubbard, B. / Serrano-Wu, M. / Kaushik, V. / Geschwindner, S. / McCarthy, M.C. / Linden, D. / Rosenmeier, J.B.
History
DepositionOct 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proprotein convertase subtilisin/kexin type 9
B: Proprotein convertase subtilisin/kexin type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5763
Polymers91,4252
Non-polymers1511
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.602, 70.121, 148.039
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proprotein convertase subtilisin/kexin type 9 / Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin- ...Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin-like protease PC9


Mass: 17035.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Proprotein convertase subtilisin/kexin type 9 / Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin- ...Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin-like protease PC9


Mass: 74389.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-A1JSM / ~{N}-(2-methylpropyl)pyrimidin-2-amine


Mass: 151.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25 mM HEPES pH 7.5 300 mM NaCl 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.759→74.02 Å / Num. obs: 39086 / % possible obs: 59.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 10.5
Reflection shellResolution: 1.759→1.984 Å / Num. unique obs: 1955 / CC1/2: 0.538

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.759→74.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1986 -RANDOM
Rwork0.1984 ---
obs0.2003 39086 59.6 %-
Displacement parametersBiso mean: 40.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.3609 Å20 Å20 Å2
2--1.4972 Å20 Å2
3----1.1363 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.759→74.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 11 325 4685
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084454HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986045HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1507SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes764HARMONIC5
X-RAY DIFFRACTIONt_it4454HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion586SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4119SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.16
LS refinement shellResolution: 1.76→1.89 Å
RfactorNum. reflection% reflection
Rfree0.3443 35 -
Rwork0.2652 --
obs0.269 782 6.2 %
Refinement TLS params.

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)
10.89850.33740.74022.4226-0.64752.66220.0770.41570.02860.4157-0.1029-0.02140.0286-0.02140.02590.0008-0.01410.0125-0.0913-0.0002-0.115231.350624.131551.5391
21.1268-0.1169-0.34820.68840.03430.95140.0574-0.02440.0205-0.02440.00760.0330.02050.033-0.065-0.0966-0.0012-0.0307-0.0542-0.0197-0.067534.830622.762619.9676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A61 - 152
2X-RAY DIFFRACTION2{ B|* }B153 - 682
3X-RAY DIFFRACTION2{ B|* }B701

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