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- PDB-6mv5: Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K) -

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Basic information

Entry
Database: PDB / ID: 6mv5
TitleAnti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)
Components
  • (Anti-PCSK9 fab 6E2 ...) x 2
  • 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 / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor 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 sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / low-density lipoprotein particle binding / LDL clearance / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / sodium channel inhibitor activity / endolysosome membrane / negative regulation of low-density lipoprotein particle clearance / signaling receptor inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of receptor internalization / apolipoprotein binding / cholesterol metabolic process / regulation of neuron apoptotic process / phospholipid metabolic process / neurogenesis / VLDLR internalisation and degradation / cholesterol homeostasis / cellular response to starvation / Post-translational protein phosphorylation / kidney development / liver development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to insulin stimulus / neuron differentiation / late endosome / positive regulation of neuron apoptotic process / 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/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 / 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: 2.1 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
DepositionOct 24, 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Anti-PCSK9 fab 6E2 heavy chain
L: Anti-PCSK9 fab 6E2 light chain
P: Proprotein convertase subtilisin/kexin type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,28010
Polymers50,7913
Non-polymers4897
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-194 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.449, 100.420, 86.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 2494.619 Da / Num. of mol.: 1 / Fragment: N-terminal peptide (UNP residues 32-53) / Mutation: E32K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NBP7

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Antibody , 2 types, 2 molecules HL

#1: Antibody Anti-PCSK9 fab 6E2 heavy chain


Mass: 24255.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Anti-PCSK9 fab 6E2 light chain


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

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Non-polymers , 4 types, 150 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 59.02 % / Description: Thick plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2018
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 36442 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 43.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.05 / Rrim(I) all: 0.089 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2 / Num. unique obs: 3626 / CC1/2: 0.627 / Rrim(I) all: 0.929 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E4Y

6e4y


Resolution: 2.1→48 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1157 3.17 %RANDOM
Rwork0.2098 ---
obs0.2107 36442 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 15 143 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043576
X-RAY DIFFRACTIONf_angle_d0.9584828
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561289
X-RAY DIFFRACTIONf_chiral_restr0.031537
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.29381380.29464357X-RAY DIFFRACTION100
2.1956-2.31130.31311280.28454344X-RAY DIFFRACTION99
2.3113-2.45610.28191380.25824369X-RAY DIFFRACTION100
2.4561-2.64580.29651480.24544354X-RAY DIFFRACTION100
2.6458-2.9120.25181540.23214366X-RAY DIFFRACTION100
2.912-3.33330.27661590.22654428X-RAY DIFFRACTION100
3.3333-4.19920.2311580.19244425X-RAY DIFFRACTION100
4.1992-48.01260.18691340.17834642X-RAY DIFFRACTION99
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)
13.8154-0.40461.51733.7812-0.3696.39950.2104-0.9841-0.55440.7928-0.08930.2460.7854-0.627-0.29410.5572-0.0698-0.13730.34920.0820.46090.61917.7821-25.203
23.1851-0.4274-0.58322.5391-0.11512.85230.1366-0.14-0.10080.32310.0538-0.246-0.03550.0224-0.16620.3568-0.0323-0.11260.23670.01880.38283.47214.5769-35.2164
34.3395-0.67781.01784.19682.19896.5259-0.20510.0354-0.13830.12650.2686-0.5349-0.33870.4873-0.22340.3881-0.0936-0.12560.30390.01860.494710.271311.6216-32.9806
44.3175-0.9325-0.21763.5748-0.06243.9851-0.1493-0.7583-0.2450.58070.1815-0.4413-0.13550.1673-0.16080.4699-0.0444-0.18640.32790.07530.43465.781712.2462-25.8037
50.3185-0.5911-0.54492.638-1.73214.87390.0354-0.288-0.0440.71550.02980.02020.1050.28590.34520.5073-0.1027-0.09080.38410.06630.3109-1.40412.349-22.6076
64.13290.3378-1.29492.102-1.01671.87160.0647-0.3876-0.31180.6402-0.15751.24030.5523-0.4978-0.05191.1055-0.08550.20140.8724-0.0790.6324-16.33999.3631-4.3957
73.0374-0.1322-0.94482.7571-0.79482.21820.2356-0.63070.22011.1516-0.14530.77970.0787-0.4583-0.15661.1323-0.04670.27970.7052-0.09150.6285-17.64614.3742-5.7264
89.6668-1.0549-2.61353.0431-0.81642.98940.06190.4324-0.2549-0.0830.0451.43820.6298-0.43450.04771.0802-0.07020.17080.6543-0.04530.9011-20.74874.0101-6.3851
94.5245-2.2951-4.40012.9531.30836.463-0.0702-0.061-0.48630.47540.21780.7751.0598-0.40380.33821.133-0.20770.43940.5811-0.01380.7578-19.44871.8981-1.5096
105.1371-1.85250.28743.84260.31952.5479-0.0103-0.28670.66850.4164-0.0573-0.2244-0.4599-0.12340.04220.3892-0.0234-0.04750.2316-0.02620.3701-7.366532.0886-32.4598
111.5199-1.0106-0.40141.9806-1.24195.423-0.0537-0.4815-0.18480.79810.33980.3918-0.102-0.2882-0.10321.11030.02950.16080.933-0.07860.5233-17.687223.75092.2881
125.4736-1.0215-0.6168.6972-4.18036.3445-0.3055-0.1775-0.9597-0.19080.55741.20690.2517-0.8615-0.38540.7243-0.1478-0.31640.77940.20421.3554-10.29979.9217-47.3933
134.997-0.4699-1.56636.9551-0.52944.40150.33410.71790.2889-0.8574-0.10960.41240.3558-1.4441-0.18640.4801-0.0218-0.11810.57850.06360.4445-5.476320.3856-48.6722
148.2606-1.20150.00872.0477-0.11576.79650.16710.21771.2079-0.72220.0678-1.2082-1.320.6343-0.09780.84070.04570.03590.4687-0.02560.67667.562225.4882-47.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 60 )
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 75 )
4X-RAY DIFFRACTION4chain 'H' and (resid 76 through 93 )
5X-RAY DIFFRACTION5chain 'H' and (resid 94 through 119 )
6X-RAY DIFFRACTION6chain 'H' and (resid 120 through 157 )
7X-RAY DIFFRACTION7chain 'H' and (resid 158 through 188 )
8X-RAY DIFFRACTION8chain 'H' and (resid 189 through 203 )
9X-RAY DIFFRACTION9chain 'H' and (resid 204 through 214 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 101 )
11X-RAY DIFFRACTION11chain 'L' and (resid 102 through 213 )
12X-RAY DIFFRACTION12chain 'P' and (resid 32 through 36 )
13X-RAY DIFFRACTION13chain 'P' and (resid 37 through 45 )
14X-RAY DIFFRACTION14chain 'P' and (resid 46 through 50 )

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