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- PDB-4nmx: PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8 -

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Basic information

Entry
Database: PDB / ID: 4nmx
TitlePCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8
Components
  • (Proprotein convertase subtilisin/kexin type 9) x 2
  • peptide 2-8
KeywordsHYDROLASE/HYDROLASE INHIBITOR / subtlisin / receptor degradation / LDL receptor / HYDROLASE-HYDROLASE INHIBITOR 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
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 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Identification of a Small Peptide That Inhibits PCSK9 Protein Binding to the Low Density Lipoprotein Receptor.
Authors: Zhang, Y. / Eigenbrot, C. / Zhou, L. / Shia, S. / Li, W. / Quan, C. / Tom, J. / Moran, P. / Di Lello, P. / Skelton, N.J. / Kong-Beltran, M. / Peterson, A. / Kirchhofer, D.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Proprotein convertase subtilisin/kexin type 9
Z: peptide 2-8


Theoretical massNumber of molelcules
Total (without water)48,5423
Polymers48,5423
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-24 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.102, 70.765, 70.413
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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


Mass: 14006.670 Da / Num. of mol.: 1 / Fragment: propeptide (UNP residues 31-152)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NBP7
#2: 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


Mass: 32836.910 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 153-452)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide peptide 2-8


Mass: 1698.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide library displayed on M13 phage
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M lithium chloride, 10% w/v PEG6000, 0.05 M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 11, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 39638 / Num. obs: 39638 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.099 / Net I/σ(I): 11
Reflection shellHighest resolution: 1.85 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTW

2qtw


Resolution: 1.85→37.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.636 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22237 1020 2.6 %RANDOM
Rwork0.18539 ---
obs0.18633 38618 99.8 %-
all-38618 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å20.05 Å2
2---0.82 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 378 3294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193035
X-RAY DIFFRACTIONr_bond_other_d0.0020.022942
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9644135
X-RAY DIFFRACTIONr_angle_other_deg0.8643.0026753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.235395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53623.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2071526
X-RAY DIFFRACTIONr_chiral_restr0.0640.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
LS refinement shellResolution: 1.85→1.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 150 -
Rwork0.256 5556 -
obs--99.34 %
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)
10.02670.02410.06250.19380.02350.2713-0.00490.01120.0108-0.0130.00440.0010.0296-0.04130.00050.0484-0.0036-0.00270.06630.00120.044913.86499.9543-16.5008
20.0418-0.01390.01850.14520.00440.00910.00040.0046-0.00090.01730.0013-0.01660.00390.0018-0.00170.05280.0016-0.00170.05480.00030.058224.439613.5408-5.1823
30.03530.0664-0.00340.18210.05610.1321-0.0010.0096-0.0022-0.02870.0094-0.0442-0.00420.0004-0.00830.04780.00220.00790.05290.00240.062531.480817.9031-19.4687
40.19080.01850.01380.4749-0.36480.3384-0.01840.00390.01690.0113-0.0184-0.0337-0.0105-0.00010.03680.0432-0.0004-0.00220.05290.00060.055118.562722.58187.8657
51.1318-1.001-0.62861.20110.91610.760.0001-0.0312-0.01840.0678-0.00990.01620.0766-0.02690.00980.06540.00260.01210.05310.0010.046610.514113.532120.1379
60.09690.0195-0.19810.1093-0.01960.4127-0.00510.0066-0.00010.0128-0.00650.00070.0194-0.00620.01150.0505-0.0025-0.00040.051-0.00190.056113.802418.854510.3622
73.9446-1.00841.23120.6551-0.57251.0681-0.04780.2214-0.1828-0.00640.03520.07420.02510.12760.01260.0606-0.00230.01960.06910.00040.049929.977713.1368-31.2549
83.48311.0827-1.05060.9556-0.26991.91420.05190.10140.1592-0.0972-0.0408-0.06730.0237-0.126-0.0110.07240.00320.00090.07880.01850.042415.267414.4426-37.1262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B176 - 260
2X-RAY DIFFRACTION2B261 - 339
3X-RAY DIFFRACTION3B340 - 446
4X-RAY DIFFRACTION4A61 - 87
5X-RAY DIFFRACTION5A88 - 105
6X-RAY DIFFRACTION6A106 - 152
7X-RAY DIFFRACTION7B153 - 163
8X-RAY DIFFRACTION8Z0 - 14

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