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- PDB-3p5b: The structure of the LDLR/PCSK9 complex reveals the receptor in a... -

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Basic information

Entry
Database: PDB / ID: 3p5b
TitleThe structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation
Components
  • (Proprotein convertase subtilisin/kexin type 9) x 2
  • Low density lipoprotein receptor variant
KeywordsHYDROLASE/LIPID BINDING PROTEIN / B-Propellor / Receptor / convertase / HYDROLASE-LIPID BINDING PROTEIN complex
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / 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 microglial cell activation ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / 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 microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / : / PCSK9-AnxA2 complex / clathrin heavy chain binding / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of triglyceride biosynthetic process / intestinal cholesterol absorption / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle receptor activity / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of protein metabolic process / lipoprotein metabolic process / LDL clearance / high-density lipoprotein particle clearance / very-low-density lipoprotein particle receptor binding / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / negative regulation of receptor internalization / : / regulation of signaling receptor activity / endolysosome membrane / sodium channel inhibitor activity / negative regulation of amyloid fibril formation / signaling receptor inhibitor activity / artery morphogenesis / cellular response to fatty acid / negative regulation of protein metabolic process / lysosomal transport / regulation of cholesterol metabolic process / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / protein autoprocessing / positive regulation of receptor internalization / apolipoprotein binding / cellular response to low-density lipoprotein particle stimulus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / regulation of neuron apoptotic process / phospholipid metabolic process / somatodendritic compartment / receptor-mediated endocytosis / cholesterol metabolic process / VLDLR internalisation and degradation / liver development / cholesterol homeostasis / cellular response to starvation / kidney development / neurogenesis / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / lipid metabolic process / neuron differentiation / cellular response to insulin stimulus / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of neuron apoptotic process / apical part of cell / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / endoplasmic reticulum lumen / lysosomal membrane
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9 / 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 / Complement Clr-like EGF-like / : ...Proprotein convertase subtilisin/kexin type 9 / 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 / Complement Clr-like EGF-like / : / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / : / Calcium-binding EGF domain / Proteinase K-like catalytic domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Laminin / : / Laminin / Coagulation Factor Xa inhibitory site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / 6 Propeller / Neuraminidase / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Alpha-Beta Plaits / Jelly Rolls / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor / Low-density lipoprotein receptor / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLo Surdo, P. / Bottomley, M.J. / Calzetta, A. / Settembre, E.C. / Cirillo, A. / Pandit, S. / Ni, Y. / Hubbard, B. / Sitlani, A. / Carfi, A.
CitationJournal: Embo Rep. / Year: 2011
Title: Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH.
Authors: Lo Surdo, P. / Bottomley, M.J. / Calzetta, A. / Settembre, E.C. / Cirillo, A. / Pandit, S. / Ni, Y.G. / Hubbard, B. / Sitlani, A. / Carfi, A.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Proprotein convertase subtilisin/kexin type 9
A: Proprotein convertase subtilisin/kexin type 9
L: Low density lipoprotein receptor variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7456
Polymers112,6243
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.000, 109.701, 178.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 10490.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NARC1, PCSK9, PSEC0052 / Cell line (production host): HEK293 / 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: 57371.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR, NARC1, PCSK9, PSEC0052 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein Low density lipoprotein receptor variant


Mass: 44762.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q59FQ1, UniProt: P01130*PLUS
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsA AND P CHAINS COME FROM THE SAME PROPROTEIN BUT ARE SEPARATE AFTER CLEAVAGE.

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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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 0.1 M sodium cacodylate pH 7.0, 1.7 M sodium acetate, 300 mM NaCl, 5% ethanol, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 23589 / Num. obs: 23117 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.298 1182 RANDOM
Rwork0.2713 --
obs0.275 23050 -
all-23453 -
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7461 0 3 0 7464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.155
X-RAY DIFFRACTIONc_bond_d0.007223
X-RAY DIFFRACTIONc_dihedral_angle_d26.5536
X-RAY DIFFRACTIONc_improper_angle_d1.76786
LS refinement shellResolution: 3.3→3.42 Å
RfactorNum. reflection% reflection
Rfree0.3588 128 -
Rwork0.3378 --
obs-2274 98.1 %

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