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- PDB-8wfr: The Crystal Structure of PCSK9 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wfr
TitleThe Crystal Structure of PCSK9 from Biortus.
Components(Proprotein convertase subtilisin/kexin type ...) x 2
KeywordsHYDROLASE / Serine protease / Apoptosis / Cholesterol metabolism / Lipid metabolism
Function / homology
Function and homology information


negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / neuron differentiation / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / late endosome / lysosome / early endosome / lysosomal membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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: 1.95 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PCSK9 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,8107
Polymers71,2632
Non-polymers5475
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-14 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.081, 70.813, 149.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Proprotein convertase subtilisin/kexin type ... , 2 types, 2 molecules AB

#1: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9


Mass: 13905.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NBP7
#2: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9


Mass: 57357.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NBP7

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Non-polymers , 4 types, 414 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.5, 20% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.26 Å / Num. obs: 49827 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.996 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3453 / CC1/2: 0.707

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.465 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2034 2469 4.962 %
Rwork0.1688 47289 -
all0.171 --
obs-49758 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.932 Å2-0 Å2-0 Å2
2---0.708 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 35 409 4737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164047
X-RAY DIFFRACTIONr_angle_refined_deg1.0171.656024
X-RAY DIFFRACTIONr_angle_other_deg0.3491.5629429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.917539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31510700
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.91310185
X-RAY DIFFRACTIONr_chiral_restr0.0460.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_nbd_refined0.1970.2737
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23667
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22089
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22347
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.220
X-RAY DIFFRACTIONr_nbd_other0.2040.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.230
X-RAY DIFFRACTIONr_mcbond_it2.9572.3412281
X-RAY DIFFRACTIONr_mcbond_other2.9572.3412281
X-RAY DIFFRACTIONr_mcangle_it4.4923.4792837
X-RAY DIFFRACTIONr_mcangle_other4.4923.4812838
X-RAY DIFFRACTIONr_scbond_it4.1632.9732155
X-RAY DIFFRACTIONr_scbond_other4.1622.9742156
X-RAY DIFFRACTIONr_scangle_it6.4814.2223184
X-RAY DIFFRACTIONr_scangle_other6.484.2233185
X-RAY DIFFRACTIONr_lrange_it8.77138.6934766
X-RAY DIFFRACTIONr_lrange_other8.69135.2614637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3011780.2643437X-RAY DIFFRACTION100
2.001-2.0550.2641630.2373365X-RAY DIFFRACTION100
2.055-2.1150.2251700.2183266X-RAY DIFFRACTION100
2.115-2.180.231570.1983186X-RAY DIFFRACTION100
2.18-2.2510.2321880.1853057X-RAY DIFFRACTION99.9692
2.251-2.330.231480.1763000X-RAY DIFFRACTION100
2.33-2.4180.1971650.1632875X-RAY DIFFRACTION100
2.418-2.5160.2171330.1632791X-RAY DIFFRACTION100
2.516-2.6280.2081580.1632675X-RAY DIFFRACTION100
2.628-2.7550.1881260.1572521X-RAY DIFFRACTION100
2.755-2.9040.1851100.152459X-RAY DIFFRACTION100
2.904-3.0790.171310.142328X-RAY DIFFRACTION100
3.079-3.2910.1921240.1542161X-RAY DIFFRACTION100
3.291-3.5530.1751120.1562028X-RAY DIFFRACTION99.8134
3.553-3.8910.174920.1511886X-RAY DIFFRACTION99.9495
3.891-4.3460.209900.1411712X-RAY DIFFRACTION100
4.346-5.0120.14780.1321543X-RAY DIFFRACTION100
5.012-6.1220.244720.1781301X-RAY DIFFRACTION99.9272
6.122-8.5890.187450.1851058X-RAY DIFFRACTION100
8.589-48.260.258290.214641X-RAY DIFFRACTION99.851

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