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- PDB-5vlh: Short PCSK9 delta-P' complex with peptide Pep1 -

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Basic information

Entry
Database: PDB / ID: 5vlh
TitleShort PCSK9 delta-P' complex with peptide Pep1
Components
  • ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2
  • CYS-ARG-LEU-PRO-TRP-ASN-LEU-GLN-ARG-ILE-GLY-LEU-PRO-CYS
  • Proprotein convertase subtilisin/kexin type 9
KeywordsHYDROLASE / proprotein convertase / subtilisin
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 / 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 / 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 / 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 / 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 / positive regulation of receptor internalization / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / 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 / 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
Similarity search - Domain/homology
Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsEigenbrot, C. / Ultsch, M.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists.
Authors: Zhang, Y. / Ultsch, M. / Skelton, N.J. / Burdick, D.J. / Beresini, M.H. / Li, W. / Kong-Beltran, M. / Peterson, A. / Quinn, J. / Chiu, C. / Wu, Y. / Shia, S. / Moran, P. / Di Lello, P. / ...Authors: Zhang, Y. / Ultsch, M. / Skelton, N.J. / Burdick, D.J. / Beresini, M.H. / Li, W. / Kong-Beltran, M. / Peterson, A. / Quinn, J. / Chiu, C. / Wu, Y. / Shia, S. / Moran, P. / Di Lello, P. / Eigenbrot, C. / Kirchhofer, D.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Source and taxonomy / Category: pdbx_audit_support / pdbx_entity_src_syn
Item: _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Oct 4, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.id
Revision 1.6Oct 16, 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
Y: CYS-ARG-LEU-PRO-TRP-ASN-LEU-GLN-ARG-ILE-GLY-LEU-PRO-CYS
Z: ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1944
Polymers53,1543
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-28 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.748, 70.748, 158.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 49784.133 Da / Num. of mol.: 1 / Fragment: residues 1-452 / Mutation: R165S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide CYS-ARG-LEU-PRO-TRP-ASN-LEU-GLN-ARG-ILE-GLY-LEU-PRO-CYS


Mass: 1671.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2


Mass: 1698.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: calcium acetate, PEG 6000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Dec 2, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→30.08 Å / Num. obs: 10763 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.149 / Net I/σ(I): 10.7
Reflection shellResolution: 2.86→2.97 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.641 / % possible all: 84.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NMX

4nmx


Resolution: 2.86→30.08 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.869 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377
RfactorNum. reflection% reflectionSelection details
Rfree0.253 442 4.11 %RANDOM
Rwork0.2 ---
obs0.202 10761 96.3 %-
Displacement parametersBiso mean: 71.47 Å2
Baniso -1Baniso -2Baniso -3
1-16.0369 Å20 Å20 Å2
2--16.0369 Å20 Å2
3----32.0738 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.86→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 5 0 2906
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082974HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034047HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1010SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it2974HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion18.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
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_contact3326SEMIHARMONIC4
LS refinement shellResolution: 2.86→3.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.271 126 4.64 %
Rwork0.215 2588 -
all0.218 2714 -
obs--87.59 %
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)
11.8238-0.0071-0.25170.8340.05810.43710.0157-0.0744-0.14070.084-0.05940.03760.0848-0.07880.0436-0.106-0.0749-0.0438-0.17220.00330.108920.988-20.08017.3836
20.72480.21960.07940.2143-0.21510-0.0183-0.0542-0.00010.06390.02260.09310.003-0.1033-0.0043-0.1357-0.10990.0861-0.0009-0.12010.14260.9073-12.311823.8978
3-0.1716-0.010.87340.54941.45711.1479-0.0098-0.05120.00370.0842-0.02590.04130.0266-0.05610.0357-0.0619-0.1375-0.05090.086-0.0774-0.07259.7083-14.366636.098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|61 - A|446}
2X-RAY DIFFRACTION2{Y|1 - Y|14}
3X-RAY DIFFRACTION3{Z|1 - Z|14}

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