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- PDB-4ov6: Crystal structure of PCSK9(53-451) with Adnectin -

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Basic information

Entry
Database: PDB / ID: 4ov6
TitleCrystal structure of PCSK9(53-451) with Adnectin
Components
  • (Proprotein convertase subtilisin/kexin type ...) x 2
  • Adnectin
KeywordsHYDROLASE/PROTEIN BINDING / PCSK9 / Adnectin / LDL-cholesterol / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / negative regulation of sodium ion transmembrane transporter activity / PCSK9-AnxA2 complex / apolipoprotein receptor binding ...low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / negative regulation of sodium ion transmembrane transporter activity / PCSK9-AnxA2 complex / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / signaling receptor inhibitor activity / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / cell-substrate junction assembly / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / proteoglycan binding / lysosomal transport / extracellular matrix structural constituent / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / positive regulation of receptor internalization / apolipoprotein binding / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / cholesterol metabolic process / VLDLR internalisation and degradation / cellular response to starvation / cell-matrix adhesion / neurogenesis / liver development / cholesterol homeostasis / 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 / integrin binding / late endosome / heart development / nervous system development / early endosome / lysosome / endoplasmic reticulum lumen / lysosomal membrane / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / RNA binding / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Peptidase S8 propeptide/proteinase inhibitor I9 / 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/S53 domain ...Peptidase S8 propeptide/proteinase inhibitor I9 / 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/S53 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Adnectin / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.69 Å
AuthorsKhan, J.A.
CitationJournal: J.Pharmacol.Exp.Ther. / Year: 2014
Title: Pharmacologic Profile of the Adnectin BMS-962476, a Small Protein Biologic Alternative to PCSK9 Antibodies for Low-Density Lipoprotein Lowering.
Authors: Mitchell, T. / Chao, G. / Sitkoff, D. / Lo, F. / Monshizadegan, H. / Meyers, D. / Low, S. / Russo, K. / DiBella, R. / Denhez, F. / Gao, M. / Myers, J. / Duke, G. / Witmer, M. / Miao, B. / ...Authors: Mitchell, T. / Chao, G. / Sitkoff, D. / Lo, F. / Monshizadegan, H. / Meyers, D. / Low, S. / Russo, K. / DiBella, R. / Denhez, F. / Gao, M. / Myers, J. / Duke, G. / Witmer, M. / Miao, B. / Ho, S.P. / Khan, J. / Parker, R.A.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Proprotein convertase subtilisin/kexin type 9
E: Proprotein convertase subtilisin/kexin type 9
F: Adnectin
G: Adnectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,20013
Polymers105,5016
Non-polymers6997
Water2,342130
1
A: Proprotein convertase subtilisin/kexin type 9
B: Proprotein convertase subtilisin/kexin type 9
F: Adnectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1317
Polymers52,7513
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-18 kcal/mol
Surface area19470 Å2
MethodPISA
2
D: Proprotein convertase subtilisin/kexin type 9
E: Proprotein convertase subtilisin/kexin type 9
G: Adnectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0696
Polymers52,7513
Non-polymers3183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-12 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.200, 118.600, 168.700
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, 4 molecules ADBE

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


Mass: 10591.213 Da / Num. of mol.: 2 / Fragment: prodomain (UNP residues 60-152)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Plasmid: pAcHLT / Cell line (production host): High Five Cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NBP7
#2: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9 / Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / ...PCSK9 / Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin-like protease PC9


Mass: 31295.355 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 153-446)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Plasmid: pAcHLT / Cell line (production host): High Five Cells / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Protein , 1 types, 2 molecules FG

#3: Protein Adnectin


Mass: 10864.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A075B5G3*PLUS

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Non-polymers , 3 types, 137 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% v/v PEG200, 1% v/v ethylene glycol, 0.1 M MES pH 6.5, crystals harvested next day, cryo-protectant: 30% v/v PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→45.03 Å / Num. all: 42093 / Num. obs: 42093 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 63.78 Å2 / Rsym value: 0.088 / Net I/σ(I): 9.4
Reflection shellResolution: 2.69→2.78 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.2 / % possible all: 86.3

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.14data extraction
MAR345data collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
BUSTER2.11.4refinement
RefinementMethod to determine structure: MIR / Resolution: 2.69→22.04 Å / Cor.coef. Fo:Fc: 0.9253 / Cor.coef. Fo:Fc free: 0.9026 / SU R Cruickshank DPI: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.258 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2110 5.04 %RANDOM
Rwork0.199 ---
all0.2006 41854 --
obs0.2006 41854 98.28 %-
Displacement parametersBiso max: 133.27 Å2 / Biso mean: 45.67 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1-8.7317 Å20 Å20 Å2
2---9.131 Å20 Å2
3---0.3993 Å2
Refine analyzeLuzzati coordinate error obs: 0.349 Å
Refinement stepCycle: LAST / Resolution: 2.69→22.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7005 0 46 130 7181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.18
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.14
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.42
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3144 122 4.57 %
Rwork0.2481 2548 -
all0.2509 2670 -
obs--98.28 %

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