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- PDB-5oca: PCSK9:Fab Complex with Dextran Sulfate -

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Basic information

Entry
Database: PDB / ID: 5oca
TitlePCSK9:Fab Complex with Dextran Sulfate
Components
  • (Fab from LDLR competitive antibody: ...Fragment antigen-binding) x 2
  • (Proprotein convertase subtilisin/kexin type ...) x 2
KeywordsHYDROLASE / PROTEIN FAB COMPLEX / AUTOCATALYTIC CLEAVAGE / CHOLESTEROL METABOLISM / DISEASE MUTATION / DISULFIDE BOND / GLYCOPROTEIN / LIPID METABOLISM / PHOSPHOPROTEIN / PROTEASE / SECRETED / SERINE PROTEASE / STEROID METABOLISM / ZYMOGEN / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / neuron differentiation / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / late endosome / lysosome / early endosome / lysosomal membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / Proteinase K-like catalytic domain / Peptidase S8/S53 domain ...Proprotein convertase subtilisin/kexin type 9 / 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 / Peptidase S8 propeptide/proteinase inhibitor I9 / Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Jelly Rolls / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heparan sulfate disaccharide / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThirup, S.S. / Vilstrup, J.P.
CitationJournal: Nat Commun / Year: 2017
Title: Heparan sulfate proteoglycans present PCSK9 to the LDL receptor.
Authors: Gustafsen, C. / Olsen, D. / Vilstrup, J. / Lund, S. / Reinhardt, A. / Wellner, N. / Larsen, T. / Andersen, C.B.F. / Weyer, K. / Li, J.P. / Seeberger, P.H. / Thirup, S. / Madsen, P. / Glerup, S.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proprotein convertase subtilisin/kexin type 9
B: Proprotein convertase subtilisin/kexin type 9
H: Fab from LDLR competitive antibody: Heavy chain
L: Fab from LDLR competitive antibody: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3417
Polymers119,5534
Non-polymers7893
Water14,196788
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-73 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.721, 137.352, 69.885
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-332-

HOH

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Components

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Proprotein convertase subtilisin/kexin type ... , 2 types, 2 molecules AB

#1: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9 / 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: 14107.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Proprotein convertase subtilisin/kexin type 9 / PCSK9 / 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: 57328.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab from LDLR competitive antibody: Heavy chain / Fragment antigen-binding


Mass: 25489.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab from LDLR competitive antibody: Light chain / Fragment antigen-binding


Mass: 22626.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 1 molecules

#5: Polysaccharide 2,3,4-tri-O-sulfo-beta-D-altropyranose-(1-6)-2,3-di-O-sulfo-alpha-L-glucopyranose / Heparan sulfate disaccharide


Type: oligosaccharide, Oligosaccharide / Class: Protein binding / Mass: 742.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Heparan sulfate disaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1211h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O][a1222h-1b_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-L-Glcp2SO33SO3]{[(6+1)][b-D-Altp2SO33SO34SO3]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 790 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1 M Tris-HCl, 0.2 M Sodium acetate, 10-15% PEG 4000, 3-6% Dextran sodium salt (Mr 5000), pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 107766 / % possible obs: 99.9 % / Redundancy: 3.5 % / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.287 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.1951 5374 4.99 %
Rwork0.1672 --
obs0.1686 107735 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7612 0 45 788 8445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097894
X-RAY DIFFRACTIONf_angle_d0.99610769
X-RAY DIFFRACTIONf_dihedral_angle_d15.7316301
X-RAY DIFFRACTIONf_chiral_restr0.0571209
X-RAY DIFFRACTIONf_plane_restr0.0061375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.32610.29111800.25213412X-RAY DIFFRACTION99
2.3261-2.35340.28961720.24573324X-RAY DIFFRACTION100
2.3534-2.38210.2931870.23913400X-RAY DIFFRACTION100
2.3821-2.41230.22851920.22453461X-RAY DIFFRACTION100
2.4123-2.4440.26011590.21283391X-RAY DIFFRACTION100
2.444-2.47750.22991890.20813396X-RAY DIFFRACTION100
2.4775-2.51290.2371660.19913411X-RAY DIFFRACTION100
2.5129-2.55040.24671800.20193387X-RAY DIFFRACTION100
2.5504-2.59020.21571630.19243440X-RAY DIFFRACTION100
2.5902-2.63270.22981890.19643339X-RAY DIFFRACTION100
2.6327-2.67810.2261800.18673454X-RAY DIFFRACTION100
2.6781-2.72670.2311860.18633396X-RAY DIFFRACTION100
2.7267-2.77920.22721530.1893417X-RAY DIFFRACTION100
2.7792-2.83590.23371680.18893427X-RAY DIFFRACTION100
2.8359-2.89750.19731790.18633431X-RAY DIFFRACTION100
2.8975-2.96490.20461580.1833412X-RAY DIFFRACTION100
2.9649-3.0390.20751830.17833433X-RAY DIFFRACTION100
3.039-3.12120.2161810.17363365X-RAY DIFFRACTION100
3.1212-3.21290.20031860.17143440X-RAY DIFFRACTION100
3.2129-3.31660.20362080.17093383X-RAY DIFFRACTION100
3.3166-3.43510.18881930.16693370X-RAY DIFFRACTION100
3.4351-3.57250.17751920.15883401X-RAY DIFFRACTION100
3.5725-3.7350.2161830.15873408X-RAY DIFFRACTION100
3.735-3.93170.17651830.15433436X-RAY DIFFRACTION100
3.9317-4.17770.16521710.14013419X-RAY DIFFRACTION100
4.1777-4.49990.16271760.12773403X-RAY DIFFRACTION100
4.4999-4.95180.14652000.12093440X-RAY DIFFRACTION100
4.9518-5.66640.15661680.14283420X-RAY DIFFRACTION99
5.6664-7.13150.1911790.17063438X-RAY DIFFRACTION100
7.1315-38.2920.18141700.17283507X-RAY DIFFRACTION99

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