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- PDB-2pmw: The Crystal Structure of Proprotein convertase subtilisin kexin t... -

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Basic information

Entry
Database: PDB / ID: 2pmw
TitleThe Crystal Structure of Proprotein convertase subtilisin kexin type 9 (PCSK9)
Components(Proprotein convertase subtilisin/kexin type 9PCSK9) x 2
KeywordsHYDROLASE / Propeptide / subtilisin / protease
Function / homology
Function and homology information


protein metabolic process => GO:0019538 / 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 / positive regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of receptor recycling / low-density lipoprotein particle clearance ...protein metabolic process => GO:0019538 / 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 / positive regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of receptor recycling / low-density lipoprotein particle clearance / PCSK9-AnxA2 complex / apolipoprotein receptor binding / negative regulation of sodium ion transmembrane transporter activity / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / LDL clearance / signaling receptor inhibitor activity / lipoprotein metabolic process / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / triglyceride metabolic process / low-density lipoprotein particle receptor binding / lysosomal transport / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / phospholipid metabolic process / regulation of neuron apoptotic process / cholesterol metabolic process / cellular response to starvation / VLDLR internalisation and degradation / neurogenesis / post-translational protein modification / cholesterol homeostasis / liver development / kidney development / Post-translational protein phosphorylation / neuron differentiation / cellular response to insulin stimulus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of neuron apoptotic process / : / 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 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / Proteinase K-like catalytic domain / Peptidase S8/S53 domain ...Proprotein convertase subtilisin/kexin type 9 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / Proteinase K-like catalytic domain / Peptidase S8/S53 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 / Jelly Rolls / Alpha-Beta Plaits / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Proprotein convertase subtilisin/kexin type 9 / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsPiper, D.E. / Romanow, W.G. / Thibault, S.T. / Walker, N.P.C.
CitationJournal: Structure / Year: 2007
Title: The Crystal Structure of PCSK9: A Regulator of Plasma LDL-Cholesterol.
Authors: Piper, D.E. / Jackson, S. / Liu, Q. / Romanow, W.G. / Shetterly, S. / Thibault, S.T. / Shan, B. / Walker, N.P.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 400COMPOUND THE MOLECULE IS EXPRESSED AS A SINGLE POLYPEPTIDE THAT UNDERGOES AUTOCATALYTIC CLEAVAGE.

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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)71,6584
Polymers71,4652
Non-polymers1922
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-40 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.106, 70.709, 150.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9 / Proprotein convertase PC9 / Subtilisin/kexin-like protease PC9 / Neural apoptosis-regulated ...Proprotein convertase PC9 / Subtilisin/kexin-like protease PC9 / Neural apoptosis-regulated convertase 1 / NARC-1


Mass: 14107.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Production host: unidentified baculovirus
References: UniProt: Q5SZQ2, UniProt: Q8NBP7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#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) / Production host: unidentified baculovirus / References: UniProt: Q5SZQ2, UniProt: Q8NBP7*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M Tris (pH 7.8) 0.2 M (NH4)2SO4 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 30097 / Num. obs: 30097 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.124 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2477 / Rsym value: 0.376 / % possible all: 81.7

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Processing

Software
NameClassification
DENZOdata reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1511 -random
Rwork0.196 ---
all-30733 --
obs-29916 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 10 215 4583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.841
LS refinement shellResolution: 2.3→2.33 Å /
RfactorNum. reflection
Rfree0.286 34
Rwork0.263 -
obs-746

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