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- PDB-3sqo: PCSK9 J16 Fab complex -

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Basic information

Entry
Database: PDB / ID: 3sqo
TitlePCSK9 J16 Fab complex
Components
  • J16 Heavy chain
  • J16 Light chain
  • PCSK9 prodomain
  • Proprotein convertase subtilisin/kexin type 9
KeywordsHYDROLASE/Immune system / cholesterol regulation / LDLR / HYDROLASE-Immune system 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 / 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 / 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 / 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 / late endosome / 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
Proprotein convertase subtilisin/kexin type 9 / 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 ...Proprotein convertase subtilisin/kexin type 9 / 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 / Jelly Rolls / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsStrop, P.
CitationJournal: J.Pharmacol.Exp.Ther. / Year: 2012
Title: Proprotein convertase substilisin/kexin type 9 antagonism reduces low-density lipoprotein cholesterol in statin-treated hypercholesterolemic nonhuman primates.
Authors: Liang, H. / Chaparro-Riggers, J. / Strop, P. / Geng, T. / Sutton, J.E. / Tsai, D. / Bai, L. / Abdiche, Y. / Dilley, J. / Yu, J. / Wu, S. / Chin, S.M. / Lee, N.A. / Rossi, A. / Lin, J.C. / ...Authors: Liang, H. / Chaparro-Riggers, J. / Strop, P. / Geng, T. / Sutton, J.E. / Tsai, D. / Bai, L. / Abdiche, Y. / Dilley, J. / Yu, J. / Wu, S. / Chin, S.M. / Lee, N.A. / Rossi, A. / Lin, J.C. / Rajpal, A. / Pons, J. / Shelton, D.L.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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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
H: J16 Heavy chain
L: J16 Light chain
P: PCSK9 prodomain


Theoretical massNumber of molelcules
Total (without water)118,5314
Polymers118,5314
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.921, 70.981, 109.156
Angle α, β, γ (deg.)90.000, 95.900, 90.000
Int Tables number4
Space group name H-MP1211

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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: 57443.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Cell line (production host): HEK293 / Production host: homo sapiens (human)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Antibody J16 Heavy chain


Mass: 23762.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody J16 Light chain


Mass: 23533.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Protein PCSK9 prodomain / 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: 13791.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS A AND P ARE EXPRESSED AS A SINGLE CHAIN. THERE IS AN AUTO-PROTEOLYSIS THAT CUTS THE CHAIN ...CHAINS A AND P ARE EXPRESSED AS A SINGLE CHAIN. THERE IS AN AUTO-PROTEOLYSIS THAT CUTS THE CHAIN INTO TWO, BUT THE SECOND CHAIN STAYS VERY TIGHTLY ASSOCIATED. IT HAS BEEN THE NOMENCLATURE OF THE PREVIOUSLY PUBLISHED PCSK9 STRUCTURES TO HAVE CHAIN P AS THE PRO-DOMAIN AND CHAIN A AS THE CATALYTIC DOMAIN
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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 7% PEG 10000, 100 mM Hepes pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 210 / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 35342 / % possible obs: 94.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.119 / Χ2: 1.133 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueΧ2% possible allMean I/σ(I) obs
2.65-2.741.90.47227260.4721.37673.5
2.74-2.852.30.51732830.5171.27188.71.71
2.85-2.982.70.46435200.4641.16994.82.32
2.98-3.1430.36536120.3651.23998
3.14-3.343.10.26636850.2661.2498.6
3.34-3.63.20.18236460.1821.20298.5
3.6-3.963.20.13436900.1341.19798.6
3.96-4.533.20.09336760.0931.13698.8
4.53-5.73.10.07437220.0741.03299
5.7-403.10.04837820.0480.7298.115.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å14.96 Å
Translation2.7 Å14.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2858 / WRfactor Rwork: 0.2264 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7844 / SU B: 32.279 / SU ML: 0.31 / SU R Cruickshank DPI: 1.7519 / SU Rfree: 0.3872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 1721 5.2 %RANDOM
Rwork0.223 ---
obs0.2261 33325 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 166.65 Å2 / Biso mean: 56.8753 Å2 / Biso min: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-1.65 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 0 32 7656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227801
X-RAY DIFFRACTIONr_bond_other_d0.0070.025261
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.95210605
X-RAY DIFFRACTIONr_angle_other_deg0.9323.00512773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60623.281317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.252151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1671555
X-RAY DIFFRACTIONr_chiral_restr0.0580.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
X-RAY DIFFRACTIONr_nbd_refined0.1890.21559
X-RAY DIFFRACTIONr_nbd_other0.1890.25325
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23686
X-RAY DIFFRACTIONr_nbtor_other0.0860.24429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.25
X-RAY DIFFRACTIONr_mcbond_it0.5561.56377
X-RAY DIFFRACTIONr_mcbond_other0.0741.52037
X-RAY DIFFRACTIONr_mcangle_it0.53928047
X-RAY DIFFRACTIONr_scbond_it0.93933241
X-RAY DIFFRACTIONr_scangle_it1.3314.52558
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 98 -
Rwork0.309 1975 -
all-2073 -
obs--83.09 %
Refinement TLS params.

Method: refined / 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)
12.29510.69070.79932.51160.06812.8159-0.12610.27510.1157-0.1680.08490.09-0.25610.03410.0412-0.15870.0357-0.0849-0.43730.004-0.2207-8.837-20.693-13.148
24.8482-1.1627-0.62335.9855-0.32365.5415-0.1474-0.5405-0.31430.8210.11630.5030.0305-0.43320.0311-0.05770.0770.0288-0.16390.0445-0.1209-28.213-31.67312.005
35.98050.84982.96433.39981.45664.4977-0.017-0.18610.01130.25460.0004-0.4128-0.03790.10280.0166-0.1335-0.0173-0.0998-0.52490.0496-0.175113.796-26.0435.267
43.69671.12513.14574.6140.74418.2790.01530.3699-0.0137-0.2475-0.0795-0.03980.35150.31090.06410.02020.047-0.0133-0.2390.0369-0.2773-13.557-20.645-48.643
53.7147-1.17022.38916.6438-3.15818.20020.12810.22340.3364-0.5348-0.2853-0.3786-0.3573-0.59240.15720.19270.21560.00830.0115-0.0283-0.1782-31.663-9.098-78.624
64.17291.18761.30116.0379-3.70847.2765-0.34050.04160.44420.15970.0133-0.5247-1.15340.53180.32720.231-0.1304-0.1504-0.18080.06230.0197-9.1970.727-46.066
79.21875.19814.35068.17390.16096.3897-0.4303-0.46110.5589-0.0921-0.33940.5178-0.8667-1.16470.76970.40110.3154-0.14060.0148-0.0649-0.0806-32.9731.955-66.391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 449
2X-RAY DIFFRACTION2A453 - 659
3X-RAY DIFFRACTION3P61 - 152
4X-RAY DIFFRACTION4L4 - 105
5X-RAY DIFFRACTION5L106 - 214
6X-RAY DIFFRACTION6H4 - 110
7X-RAY DIFFRACTION7H111 - 212

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