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- PDB-6u2f: PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacy... -

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Basic information

Entry
Database: PDB / ID: 6u2f
TitlePCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2
Components
  • 7G7 heavy chain
  • 7G7 light chain
  • Organo-peptide PCSK9 inhibitor
  • Proprotein convertase subtilisin/kexin type 9
KeywordsHYDROLASE/HYDROLASE INHIBITOR/IMMUNE SYSTEM / Inhibitor / complex / HYDROLASE-HYDROLASE INHIBITOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / 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 / low-density lipoprotein particle receptor binding / triglyceride metabolic process / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / immunoglobulin complex, circulating / immunoglobulin receptor binding / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / kidney development / complement activation, classical pathway / cholesterol homeostasis / antigen binding / 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 / antibacterial humoral response / lysosome / early endosome / blood microparticle / immune response / 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 exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / Proteinase K-like catalytic domain / Peptidase S8/S53 domain ...Proprotein convertase subtilisin/kexin type 9 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Jelly Rolls / Alpha-Beta Plaits / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Inhibitor, Oligopeptide / MAb 6H10 light chain / Ighg protein / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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 19, 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 1.2Aug 12, 2020Group: Derived calculations / Structure summary
Category: pdbx_molecule_features / pdbx_struct_conn_angle ...pdbx_molecule_features / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / 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 / _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: Organo-peptide PCSK9 inhibitor
H: 7G7 heavy chain
L: 7G7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8115
Polymers124,7714
Non-polymers401
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-56 kcal/mol
Surface area43120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.569, 142.740, 239.287
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) / References: UniProt: Q569X1
#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: 75508.445 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 Organo-peptide PCSK9 inhibitor


Type: Oligopeptide / Class: Inhibitor / Mass: 1485.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Inhibitor, Oligopeptide

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Non-polymers , 2 types, 14 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.: 13 / 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: 3.78 Å3/Da / Density % sol: 71.15 % / 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 / Temp details: room temp

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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: Oct 4, 2017 / Details: Liquid Crystal
RadiationMonochromator: liquid nitrogen-cooled 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: 2.94→49.37 Å / Num. obs: 40663 / % possible obs: 94.16 % / Redundancy: 4.6 % / Biso Wilson estimate: 60.8 Å2 / CC1/2: 0.986 / Rsym value: 0.141 / Net I/σ(I): 11
Reflection shellResolution: 2.94→3.05 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2762 / CC1/2: 0.542 / Rsym value: 0.902 / % possible all: 69

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VLP

5vlp


Resolution: 2.94→49.37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.513 / SU Rfree Blow DPI: 0.275
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1958 5.12 %RANDOM
Rwork0.174 ---
obs0.175 38269 94.2 %-
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 60.57 Å2 / Biso min: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.0848 Å20 Å20 Å2
2--1.7979 Å20 Å2
3----1.7131 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.94→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7757 0 111 13 7881
Biso mean--60.09 49.43 -
Num. residues----1022
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3309SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2532HARMONIC5
X-RAY DIFFRACTIONt_it15605HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1056SEMIHARMONIC5
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_contact16469SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15605HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg28122HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion16.73
LS refinement shellResolution: 2.94→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3481 47 6.14 %
Rwork0.2175 719 -
all0.2252 766 -
obs--57.16 %
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)
10.14260.2707-0.39720.27760.15050.0179-0.0010.0005-0.0018-0.0031-0.00050.00260.00190.00010.00140.0009-0.00130.006-0.008-0.00110.004921.81320.415467.164
200.122-0.3260-0.14090.1744-0.0005-0.00090.0020.0034-0.00010.00550.0005-0.00190.00060.0021-0.0080.0174-0.00390.00380.003116.295532.740186.9201
300.386-0.24270.1591-0.14270.0734-0.0001-0.0025-0.00260.0022-0.0031-0.0014-0.00340.00090.0032-0.0022-0.00880.00360.00050.01210.003629.480138.729477.5919
40.05070.4196-0.35870.7316-0.4130.09510.001-0.00120.00170.0104-0.0041-0.00120.00120.00330.003-0.0083-0.0140.0183-0.00790.01760.000935.329448.123772.9581
50.022-0.04150.07710.0392-0.08110.086-0.0004-0.0004-0.00030.0002-0.00030.0004-0.00110.00130.0007-0.0011-0.00020.00260.0016-0.0013-0.002241.241462.179251.0607
60.07230.1558-0.16740.1018-0.11910.10930.00070.0016-0.00050.0028-0.0011-0.0007-0.00070.00120.00050.002-0.00270.00140.00210.0014-0.000450.471861.170158.2172
70.00680.05720.08530.04630.01910.02860.0003-0.00050.00020.002-0.0005-0.0009-0.00010.00160.00020.0013-0.00820.0009-0.0025-0.00410.00146.851660.235867.6207
800.00540.00050.00140.00980.0031-0-00.00030.00010.0001-0.0001-0-0.0001-0.00010.0017-0.00320.0015-0.0005-0.0013-0.000527.055355.153893.2808
90.0018-0.0089-0.07260.0080.02640.04930.0001-00.0005-00.0002-0.00010.00070.0012-0.00030.0023-0.00010.0012-0.0006-0.0013-0.000252.076947.228621.4039
100-0.0241-0.05510.20910.24140.33350.0011-0.0067-0.0015-0.01070.00340.00570.00580.0093-0.0045-0.00260.0002-0.01330.0041-0.007-0.006248.474751.372326.3511
1100.15470.26230.13730.25720.08180.00040.00090.00290.0001-0.0005-0.00260.00040.001200.0058-0.0074-0.0175-0.005-0.0081-0.003442.48349.5825-0.7808
120.07880.1070.00330.0141-0.03060.00260.0002-0.0008-0.001-0.001-0.00080.0003-0.0012-0.00050.0006-0.0007-0.0036-0.00230.00210.00060.001725.31463.548528.6232
130.086-0.01080.15920.0379-0.03580.0893-0-00.0003-0.0022-0.00060.00190.0005-0.00030.00060.0001-0.0006-0.00540.0038-0.006-0.002435.496567.829529.1217
140-0.10040.06240.15470.15210.04140.0002-0.0013-0.0005-0.0007-0.00080.0021-0.0008-0.00020.00070.004-0.0025-0.0068-0.0003-0.0049-0.00332.096362.620123.4277
150-0.16960.310500.10140.1534-0.001-0.0018-0.00130.00220.00030.0012-0.0003-0.00550.00070.0043-0.0078-0.0199-0.0002-0.0089-0.008828.107746.2333-2.1128
160.0192-0.05080.174300.12830.0022-0.00010.00020.0015-0.00030.00070.00120.0001-0.0018-0.0007-0.0007-0.0029-0.00790.0019-0.0054-0.001822.354346.4378-10.2527
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|2 - 11}B2 - 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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