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- PDB-6e4z: Anti-PCSK9 fab 6E2 bound to the modified N-terminal peptide from PCSK9 -

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Basic information

Entry
Database: PDB / ID: 6e4z
TitleAnti-PCSK9 fab 6E2 bound to the modified N-terminal peptide from PCSK9
Components
  • 6E2 heavy chain
  • 6E2 light chain
  • Proprotein convertase subtilisin/kexin type 9
KeywordsIMMUNE SYSTEM / Antibody / Hydrolase / PCSK9 / FAB 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 / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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 ...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, 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Anti-lox-1 15C4 light chain / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsUltsch, M.H. / Kirchhofer, D.K.
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain.
Authors: Ultsch, M. / Li, W. / Eigenbrot, C. / Di Lello, P. / Lipari, M.T. / Gerhardy, S. / AhYoung, A.P. / Quinn, J. / Franke, Y. / Chen, Y. / Kong Beltran, M. / Peterson, A. / Kirchhofer, D.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 6E2 heavy chain
L: 6E2 light chain
P: Proprotein convertase subtilisin/kexin type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3489
Polymers50,9253
Non-polymers4236
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-200 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.929, 99.782, 86.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-446-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide 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: 2628.558 Da / Num. of mol.: 1 / Fragment: UNP residues 32-53 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NBP7

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Antibody , 2 types, 2 molecules HL

#1: Antibody 6E2 heavy chain


Mass: 24255.182 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4
#2: Antibody 6E2 light chain


Mass: 24040.912 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4 / References: UniProt: A0A097PUG4

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Non-polymers , 3 types, 128 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 15% w/v PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2014
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: 2.2→33.42 Å / Num. obs: 31726 / % possible obs: 99.78 % / Redundancy: 7.3 % / CC1/2: 0.657 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 20.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3101 / CC1/2: 0.657 / Rpim(I) all: 0.352 / Rrim(I) all: 0.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E4Y

6e4y


Resolution: 2.202→33.417 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2359 1060 3.35 %
Rwork0.1951 --
obs0.1965 31636 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→33.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 10 122 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023544
X-RAY DIFFRACTIONf_angle_d1.0394808
X-RAY DIFFRACTIONf_dihedral_angle_d13.5412102
X-RAY DIFFRACTIONf_chiral_restr0.054535
X-RAY DIFFRACTIONf_plane_restr0.006610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2018-2.30190.31341190.27053707X-RAY DIFFRACTION98
2.3019-2.42330.27251220.2363780X-RAY DIFFRACTION100
2.4233-2.5750.26571260.22913775X-RAY DIFFRACTION100
2.575-2.77380.2781340.22723808X-RAY DIFFRACTION100
2.7738-3.05270.2681280.22793806X-RAY DIFFRACTION100
3.0527-3.49410.28021320.21083837X-RAY DIFFRACTION100
3.4941-4.40060.19731560.17163850X-RAY DIFFRACTION100
4.4006-33.42040.21411430.17014013X-RAY DIFFRACTION100
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)
11.66750.45640.45332.0305-0.29082.14710.06140.08320.1364-0.23910.0325-0.224-0.03520.0865-0.09220.31380.05650.10610.30820.0250.36984.188336.6349-12.4311
23.69521.372-0.94643.23520.29572.7993-0.04680.1777-0.4944-0.1733-0.0428-0.14770.4326-0.16770.0810.32450.02090.03770.28020.00780.3545-8.09217.7578-11.571
31.58551.04380.58091.72570.15171.5852-0.21030.06880.5088-0.87670.03880.9204-0.4582-0.35420.13850.92130.0445-0.27320.594-0.06750.6674-17.099841.3125-38.5206
41.40080.9508-0.06871.8312-0.06932.1572-0.20540.46160.1386-0.55560.27050.13750.0169-0.1925-0.08570.9049-0.0669-0.16490.76320.00310.5271-17.958326.8299-46.8315
57.35262.5370.67085.1914-0.218.16750.0667-1.1774-0.7110.8379-0.2388-0.37790.2914-0.66540.16550.4614-0.06590.05610.52240.10660.4065-1.976228.13075.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:114)
2X-RAY DIFFRACTION2(chain L and resid 1:107)
3X-RAY DIFFRACTION3(chain H and resid 115:214)
4X-RAY DIFFRACTION4(chain L and resid 108:213)
5X-RAY DIFFRACTION5(chain P)

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