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- PDB-3bps: PCSK9:EGF-A complex -

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Basic information

Entry
Database: PDB / ID: 3bps
TitlePCSK9:EGF-A complex
Components
  • (Proprotein convertase subtilisin/kexin type 9) x 2
  • Low-density lipoprotein receptor
KeywordsHYDROLASE/Lipid Transport / PCSK9 / LDL receptor / Autocatalytic cleavage / Cholesterol metabolism / Disease mutation / Glycoprotein / Hydrolase / Lipid metabolism / Phosphoprotein / Protease / Secreted / Serine protease / Steroid metabolism / Zymogen / Coated pit / EGF-like domain / Endocytosis / Host-virus interaction / Lipid transport / Membrane / Transmembrane / Transport / HYDROLASE-Lipid Transport COMPLEX
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / 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 microglial cell activation / negative regulation of sodium ion import across plasma membrane ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / 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 microglial cell activation / negative regulation of sodium ion import across plasma membrane / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / PCSK9-AnxA2 complex / low-density lipoprotein particle clearance / positive regulation of triglyceride biosynthetic process / clathrin heavy chain binding / negative regulation of receptor recycling / apolipoprotein receptor binding / intestinal cholesterol absorption / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / response to caloric restriction / LDL clearance / lipoprotein metabolic process / high-density lipoprotein particle clearance / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / endolysosome membrane / sodium channel inhibitor activity / cellular response to fatty acid / negative regulation of amyloid fibril formation / negative regulation of low-density lipoprotein particle clearance / signaling receptor inhibitor activity / regulation of cholesterol metabolic process / artery morphogenesis / negative regulation of protein metabolic process / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / protein autoprocessing / positive regulation of receptor internalization / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / retinoid metabolic process / cholesterol metabolic process / Retinoid metabolism and transport / regulation of neuron apoptotic process / phospholipid metabolic process / clathrin-coated pit / neurogenesis / somatodendritic compartment / receptor-mediated endocytosis / VLDLR internalisation and degradation / cholesterol homeostasis / cellular response to starvation / Post-translational protein phosphorylation / kidney development / clathrin-coated endocytic vesicle membrane / liver development / lipid metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to insulin stimulus / neuron differentiation / positive regulation of inflammatory response / apical part of cell / late endosome / Cargo recognition for clathrin-mediated endocytosis / positive regulation of neuron apoptotic process / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / endoplasmic reticulum lumen / negative regulation of gene expression / lysosomal membrane / external side of plasma membrane
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 / Complement Clr-like EGF-like / : ...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 / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Laminin / Laminin / : / Coagulation Factor Xa inhibitory site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Alpha-Beta Plaits / Jelly Rolls / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsKwon, H.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular basis for LDL receptor recognition by PCSK9.
Authors: Kwon, H.J. / Lagace, T.A. / McNutt, M.C. / Horton, J.D. / Deisenhofer, J.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Proprotein convertase subtilisin/kexin type 9
A: Proprotein convertase subtilisin/kexin type 9
E: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8584
Polymers77,8183
Non-polymers401
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.952, 116.952, 134.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Proprotein convertase subtilisin/kexin type 9 / 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: 11283.910 Da / Num. of mol.: 1 / Fragment: Prodomain, UNP residues 53-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Production host: Escherichia coli (E. coli) / Strain (production host): HEK293S
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Proprotein convertase subtilisin/kexin type 9 / 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: 57443.730 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 153-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1 / Production host: Escherichia coli (E. coli) / Strain (production host): HEK293S
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 9090.130 Da / Num. of mol.: 1
Fragment: EGF-like 1, EGF-like 2 domains, UNP residues 314-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Escherichia coli (E. coli) / References: UniProt: P01130
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 294 K / pH: 4.8
Details: 0.3M (NH4)H2PO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 4.80

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2007 / Details: SI
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 36583 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.8 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P4E

2p4e


Resolution: 2.41→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.374 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1831 5 %RANDOM
Rwork0.203 ---
obs0.205 34679 99 %-
all-34679 --
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.41→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 1 129 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9595935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19723.118186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72615705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681539
X-RAY DIFFRACTIONr_chiral_restr0.0980.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21728
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22897
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.52875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51624502
X-RAY DIFFRACTIONr_scbond_it2.17631656
X-RAY DIFFRACTIONr_scangle_it3.4894.51433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 122 -
Rwork0.259 2326 -
obs--91.21 %
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)
11.052-0.0820.29771.57560.00532.6158-0.0690.05410.1140.030.2039-0.04410.1249-0.1448-0.1349-0.1980.0099-0.0208-0.16030.0818-0.153831.4077-8.16990.0071
23.9852-0.0886-1.84995.80.42525.0391-0.08940.35460.2015-0.11380.37750.4197-0.1482-0.4655-0.2881-0.1683-0.0352-0.0161-0.06240.19-0.108629.50289.3393-25.2765
310.22651.1566-0.4935.9805-1.066311.68050.00250.1504-0.29880.18280.00720.69170.7761-0.9287-0.00960.1912-0.3736-0.10070.05740.1747-0.043213.6469-34.4849-1.305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1PA61 - 1529 - 100
2X-RAY DIFFRACTION1AB153 - 4491 - 297
3X-RAY DIFFRACTION2AB453 - 682301 - 530
4X-RAY DIFFRACTION3EC292 - 3323 - 43
5X-RAY DIFFRACTION3ED11
6X-RAY DIFFRACTION3EG3731

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