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- PDB-6u3i: Design of organo-peptides as bipartite PCSK9 antagonists -

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Basic information

Entry
Database: PDB / ID: 6u3i
TitleDesign of organo-peptides as bipartite PCSK9 antagonists
Components
  • 7G7 heavy chain
  • 7G7 light chain
  • Proprotein convertase subtilisin/kexin type 9
  • cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)I(D-ser)LLR - NH2
KeywordsHYDROLASE/HYDROLASE INHIBITOR/IMMUNE SYSTEM / Inhibitor / complex / HYDROLASE-HYDROLASE INHIBITOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / PCSK9-LDLR complex / PCSK9-AnxA2 complex / : / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding ...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 / PCSK9-LDLR complex / PCSK9-AnxA2 complex / : / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / LDL clearance / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of receptor internalization / : / regulation of signaling receptor activity / endolysosome membrane / sodium channel inhibitor activity / signaling receptor inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / protein autoprocessing / positive regulation of receptor internalization / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / regulation of neuron apoptotic process / phospholipid metabolic process / neurogenesis / cholesterol metabolic process / VLDLR internalisation and degradation / cholesterol homeostasis / liver development / cellular response to starvation / kidney development / Post-translational protein phosphorylation / cellular response to insulin stimulus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron differentiation / 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 / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / RNA binding / 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 propeptide/proteinase inhibitor I9 ...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 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / : / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Alpha-Beta Plaits / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MAb 6H10 light chain / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsUltsch, M.H. / Kirchhofer, D.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Design of Organo-Peptides As Bipartite PCSK9 Antagonists.
Authors: Burdick, D.J. / Skelton, N.J. / Ultsch, M. / Beresini, M.H. / Eigenbrot, C. / Li, W. / Zhang, Y. / Nguyen, H. / Kong-Beltran, M. / Quinn, J.G. / Kirchhofer, D.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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: cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)I(D-ser)LLR - NH2
H: 7G7 heavy chain
L: 7G7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8995
Polymers124,8594
Non-polymers401
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-56 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.570, 143.030, 241.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 2 types, 2 molecules HL

#3: Antibody 7G7 heavy chain


Mass: 24117.857 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody 7G7 light chain


Mass: 23659.061 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: A0A0U5BC76

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 / PCSK9


Mass: 75566.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)I(D-ser)LLR - NH2


Mass: 1515.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 27 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.85 Å3/Da / Density % sol: 71.64 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2018 / Details: Si 111
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→49.74 Å / Num. obs: 43160 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.16 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4478 / CC1/2: 0.652 / Rsym value: 1.009 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VLP

5vlp


Resolution: 2.9→48.2 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.403 / SU Rfree Blow DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2197 5.1 %RANDOM
Rwork0.179 ---
obs0.181 43105 99.9 %-
Displacement parametersBiso max: 151.77 Å2 / Biso mean: 57.58 Å2 / Biso min: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1--28.431 Å20 Å20 Å2
2--13.3427 Å20 Å2
3---15.0884 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7772 0 111 26 7909
Biso mean--57.54 45.5 -
Num. residues----1024
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3316SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2535HARMONIC5
X-RAY DIFFRACTIONt_it15623HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1059SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16225SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15623HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg28150HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion16.64
LS refinement shellResolution: 2.9→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3618 39 4.52 %
Rwork0.2588 824 -
all0.2638 863 -
obs--99.32 %
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)
10.11050.2912-0.35110.7460.60450.2406-0.00280.0031-0.0187-0.01720.00660.01130.00190.0018-0.0038-0.00520.02070.0123-0.04110.00310.011721.952120.28867.7405
200.2374-0.56610-0.34510.503-0.0028-0.00230.01480.01110.00130.02870.0039-0.01410.00150-0.02090.0651-0.02270.01530.010716.424832.665687.4886
30.00120.6126-0.51780.471-0.1480.0098-0.0017-0.005-0.01050.0032-0.0084-0.0054-0.01230.00420.01-0.02-0.01920.0255-0.01660.05180.020429.619538.70578.1124
40.40880.5912-0.50140.4767-0.42840.57880.00550.009-0.00480.0366-0.00950.01810.00880.01890.0039-0.0368-0.01340.0331-0.03920.0334-0.017235.54548.15373.4481
50.0817-0.1810.36950.0441-0.27170.5462-0.0018-0.0020.0003-0.00170.0010.0102-0.00450.00030.0008-0.0075-0.00520.00120.0053-0.0082-0.00841.551662.231151.4582
60.09580.1738-0.08660.0784-0.27360.37910.00450.00940.00870.009-0.0115-0.00120.00480.0090.007-0.0014-0.0017-0.0171-0.00490.0051-0.012150.830761.271658.6444
700.10930.1180.0501-0.19380.3070.0012-0.0006-0.00270.0118-0.0008-0.0036-0.0050.0067-0.00030.003-0.02490.0004-0.0093-0.0167-0.002147.116260.307468.0546
800.02140.0130.01440.07930.0113-0.00040.00010.00090.00050.0006-0.0001-0.00140.0001-0.00020.006-0.01530.0114-0.0058-0.0134-0.001326.695654.529194.5599
90.0102-0.0333-0.22290.02840.10090.13460.00110.00040.0008-0.00040.001200.00130.0073-0.00230.00690.00610.0061-0.00420.0043-0.004152.65347.501621.6399
1000.0929-0.11330.0060.47051.18810.0047-0.034-0.0129-0.03540.01490.03270.03420.0522-0.0196-0.01720.0314-0.04640.0114-0.0028-0.0348.99451.542626.5469
110.01130.51611.03060.5170.65190.49070.0030.00550.03070.00290.0044-0.0189-0.01260.0101-0.00740.0265-0.023-0.0767-0.0088-0.01080.003642.967749.8557-0.9413
120.22250.26110.03250.0376-0.04190.05820.0003-0.0016-0.0023-0.0029-0.00360.0048-0.003-0.00410.00330.0011-0.0105-0.01290.0037-0.0010.006725.766963.549928.8569
130.2549-0.17810.58060.1123-0.05960.34450.0001-0.00050-0.0118-0.00550.01-0.0022-0.00180.0054-0.00660.0039-0.00980.0034-0.0155-0.009435.942667.911829.449
140-0.21510.38140.36110.34650.12730.0003-0.0136-0.0169-0.0066-0.00830.0051-0.00340.00150.0080.00650.0001-0.0298-0.0095-0.0087-0.006432.585862.657823.6806
150-0.30460.866200.39950.6234-0.0059-0.0111-0.00320.0061-0.0037-0.00010.0034-0.02480.00960.0176-0.0352-0.0836-0.0033-0.0325-0.035128.590146.3818-2.2797
160.0961-0.16430.739100.50560.0888-0.00040.00180.0049-0.0020.00420.00550.0012-0.0089-0.0038-0.002-0.0132-0.03460.0105-0.0254-0.008922.826846.6157-10.4075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|61 - 186}A61 - 186
2X-RAY DIFFRACTION2{A|187 - 277}A187 - 277
3X-RAY DIFFRACTION3{A|278 - 359}A278 - 359
4X-RAY DIFFRACTION4{A|360 - 528}A360 - 528
5X-RAY DIFFRACTION5{A|529 - 566}A529 - 566
6X-RAY DIFFRACTION6{A|567 - 625}A567 - 625
7X-RAY DIFFRACTION7{A|626 - 682}A626 - 682
8X-RAY DIFFRACTION8{B|1 - 11}B1 - 11
9X-RAY DIFFRACTION9{H|1 - 17}H1 - 17
10X-RAY DIFFRACTION10{H|18 - 145}H18 - 145
11X-RAY DIFFRACTION11{H|146 - 222}H146 - 222
12X-RAY DIFFRACTION12{L|1 - 25}L1 - 25
13X-RAY DIFFRACTION13{L|26 - 76}L26 - 76
14X-RAY DIFFRACTION14{L|77 - 110}L77 - 110
15X-RAY DIFFRACTION15{L|111 - 187}L111 - 187
16X-RAY DIFFRACTION16{L|188 - 214}L188 - 214

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