[English] 日本語
Yorodumi
- PDB-8vdv: pcsk9 in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vdv
Titlepcsk9 in complex with inhibitor
Components
  • (Proprotein convertase subtilisin/kexin type 9) x 2
  • Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH
KeywordsHYDROLASE/INHIBITOR / cyclic peptide / 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
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: 1.972 Å
AuthorsXu, M. / Chopra, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PCSK9 in complex with inhibitor
Authors: Xu, M. / Xu, M.
History
DepositionDec 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proprotein convertase subtilisin/kexin type 9
B: Proprotein convertase subtilisin/kexin type 9
L: Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH


Theoretical massNumber of molelcules
Total (without water)67,8333
Polymers67,8333
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-25 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.086, 70.846, 149.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 10490.109 Da / Num. of mol.: 1 / Fragment: PRODOMAIN, UNP RESIDUES 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Homo sapiens (human)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#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: 56107.277 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 153-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Homo sapiens (human)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH


Type: Cyclic peptide / Class: Inhibitor / Mass: 1235.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002534
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 20.0% Peg-6000, 0.1M Tris pH8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.972→149.007 Å / Num. obs: 47937 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 15.1 / Num. measured all: 307800
Reflection shellResolution: 1.972→1.978 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.631 / Num. measured all: 3285 / Num. unique obs: 496 / Rpim(I) all: 0.264 / Rrim(I) all: 0.685 / Net I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.972→58.094 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 2426 5.07 %
Rwork0.1857 --
obs0.1872 47859 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.972→58.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 89 258 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014476
X-RAY DIFFRACTIONf_angle_d1.526056
X-RAY DIFFRACTIONf_dihedral_angle_d15.3381609
X-RAY DIFFRACTIONf_chiral_restr0.091695
X-RAY DIFFRACTIONf_plane_restr0.009787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.972-2.01170.29121710.22062607X-RAY DIFFRACTION100
2.0117-2.05550.24991440.21252611X-RAY DIFFRACTION100
2.0555-2.10330.22661550.20292642X-RAY DIFFRACTION100
2.1033-2.15590.22891410.19122642X-RAY DIFFRACTION100
2.1559-2.21420.24991410.18852627X-RAY DIFFRACTION100
2.2142-2.27940.23721350.19792650X-RAY DIFFRACTION100
2.2794-2.35290.25061460.192633X-RAY DIFFRACTION100
2.3529-2.4370.23741450.18742663X-RAY DIFFRACTION100
2.437-2.53460.19891310.19172661X-RAY DIFFRACTION100
2.5346-2.650.22511360.20292648X-RAY DIFFRACTION100
2.65-2.78970.24811430.19862673X-RAY DIFFRACTION100
2.7897-2.96440.21241340.18742678X-RAY DIFFRACTION100
2.9644-3.19330.20361400.19052661X-RAY DIFFRACTION100
3.1933-3.51460.18441340.18072733X-RAY DIFFRACTION100
3.5146-4.02310.21131490.16982685X-RAY DIFFRACTION100
4.0231-5.06820.17721390.15972740X-RAY DIFFRACTION99
5.0682-58.0940.2311420.19412879X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more