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- PDB-2w2o: PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR -

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Basic information

Entry
Database: PDB / ID: 2w2o
TitlePCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR
Components
  • (PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9) x 2
  • LOW-DENSITY LIPOPROTEIN RECEPTOR
KeywordsHYDROLASE/RECEPTOR / HYDROLASE-RECEPTOR COMPLEX / PCSK9 / LDLR / PROPROTEIN CONVERTASE / LOW-DENSITY LIPOPROTEIN RECEPTOR / EGF / CARDIOVASCULAR DISEASE / FAMILIAL HYPERCHOLESTEROLEMIA / LIPID METABOLISM / SERINE PROTEASE / HYDROLASE / LIPID TRANSPORT / STEROID METABOLISM / RECEPTOR
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / negative regulation of astrocyte activation / positive regulation of lysosomal protein catabolic process / 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 / negative regulation of astrocyte activation / positive regulation of lysosomal protein catabolic process / 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 / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / response to caloric restriction / positive regulation of low-density lipoprotein particle receptor catabolic process / 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 / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle / cholesterol transport / negative regulation of receptor internalization / endolysosome membrane / sodium channel inhibitor activity / cellular response to fatty acid / negative regulation of amyloid fibril formation / 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 / COPII-coated ER to Golgi transport vesicle / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / protein autoprocessing / regulation of neuron apoptotic process / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / long-term memory / phagocytosis / retinoid metabolic process / Retinoid metabolism and transport / VLDLR internalisation and degradation / phospholipid metabolic process / clathrin-coated pit / neurogenesis / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / cellular response to starvation / Post-translational protein phosphorylation / kidney development / clathrin-coated endocytic vesicle membrane / liver development / lipid metabolic process / cellular response to insulin stimulus / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / neuron differentiation / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / late endosome / Clathrin-mediated endocytosis / positive regulation of neuron apoptotic process / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / endosome membrane / receptor complex / endoplasmic reticulum lumen / lysosomal membrane / negative regulation of gene expression / serine-type endopeptidase activity
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 / Complement Clr-like EGF-like / Peptidase S8 propeptide/proteinase inhibitor I9 ...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 / Complement Clr-like EGF-like / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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. / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / 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/S53 domain / Laminin / Subtilase family / Laminin / Coagulation Factor Xa inhibitory site / 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 / 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: 2.62 Å
AuthorsBottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. ...Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Biochemical Characterization of the Wild Type Pcsk9/Egf-Ab Complex and Natural Fh Mutants.
Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. ...Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
History
DepositionNov 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
E: LOW-DENSITY LIPOPROTEIN RECEPTOR
P: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9714
Polymers57,9313
Non-polymers401
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area22210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.948, 85.948, 218.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 ...PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1


Mass: 33156.312 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR / LDL RECEPTOR


Mass: 12095.453 Da / Num. of mol.: 1 / Fragment: EGF-A DOMAIN, RESIDUES 314-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01130
#3: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED ...PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1


Mass: 12679.604 Da / Num. of mol.: 1 / Fragment: PROPEPTIDE, RESIDUES 53-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NBP7
#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.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 374 TO TYR
Has protein modificationY
Sequence detailsHUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ARE A RESULT OF THE CLONING PROCEDURE. ...HUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ARE A RESULT OF THE CLONING PROCEDURE. THE 15TH RESIDUE CORRESPONDS TO ALA53 OF WT PCSK9. HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES ARE A LINKER AND A 6HIS TAG, RESULTING FROM THE CLONING PROCEDURE. THE FIRST RESIDUE CORRESPONDS TO SER153 OF WT PCSK9. HUMAN LDLR EGF-AB DOMAINS. THE FIRST 27 RESIDUES IN THE SEQUENCE ARE A 6HIS TAG AND A LINKER FROM THE CLONING PROCEDURE. THE 28TH RESIDUE CORRESPONDS TO GLY293 OF WT LDLR.

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.62→40 Å / Num. obs: 25321 / % possible obs: 99.5 % / Observed criterion σ(I): 3.5 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTW

2qtw


Resolution: 2.62→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 26.361 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26311 1287 5.1 %RANDOM
Rwork0.22659 ---
obs0.22843 23984 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.196 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å20 Å20 Å2
2--4.13 Å20 Å2
3----8.25 Å2
Refinement stepCycle: LAST / Resolution: 2.62→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 1 19 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223212
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9664369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50423.723137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11915518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1411524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022428
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22158
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4011.52107
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73423313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89231215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4924.51054
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.373 92
Rwork0.372 1741
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)
11.8564-0.4178-0.32112.4408-1.82626.45530.0664-0.05750.03740.2475-0.3446-0.069-0.57820.93840.27830.0176-0.1374-0.05360.52480.11820.1424-15.9634-3.197430.006
26.3963-0.1454-5.74044.52180.07116.9332-0.4772-0.281-0.59340.1560.24880.1184-0.0153-0.11510.2284-0.19360.1375-0.02580.94490.17330.1428-0.1491-15.21429.5934
32.5660.4558-2.42882.4724-2.05779.3209-0.0106-0.0027-0.00330.4345-0.11930.1445-0.33740.51560.12990.098-0.02760.01130.32070.05350.1544-30.2104-15.391852.3589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 446
2X-RAY DIFFRACTION2E285 - 332
3X-RAY DIFFRACTION3P60 - 152

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