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- PDB-5jxj: Structure of the proprotein convertase furin complexed to meta-gu... -

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Basic information

Entry
Database: PDB / ID: 5jxj
TitleStructure of the proprotein convertase furin complexed to meta-guanidinomethyl-Phac-RVR-Amba in presence of EDTA
Components
  • 2UC-ARG-VAL-ARG-00S
  • Furin
KeywordsHYDROLASE / protease / inhibitor / proteolysis
Function / homology
Function and homology information


furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / : / negative regulation of low-density lipoprotein particle receptor catabolic process ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / : / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / nerve growth factor binding / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / secretion by cell / Signaling by PDGF / trans-Golgi network transport vesicle / Signaling by NODAL / heparan sulfate binding / blastocyst formation / Elastic fibre formation / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / peptide hormone processing / CD163 mediating an anti-inflammatory response / Activation of Matrix Metalloproteinases / regulation of protein catabolic process / Collagen degradation / Maturation of hRSV A proteins / TGF-beta receptor signaling activates SMADs / collagen catabolic process / Respiratory syncytial virus (RSV) attachment and entry / Uptake and function of anthrax toxins / extracellular matrix disassembly / regulation of signal transduction / endopeptidase activator activity / Removal of aminoterminal propeptides from gamma-carboxylated proteins / viral life cycle / extracellular matrix organization / peptide binding / serine-type peptidase activity / transforming growth factor beta receptor signaling pathway / protein maturation / negative regulation of inflammatory response to antigenic stimulus / serine-type endopeptidase inhibitor activity / trans-Golgi network / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / protein processing / Golgi lumen / peptidase activity / heparin binding / protease binding / endopeptidase activity / viral translation / amyloid fibril formation / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / Attachment and Entry / positive regulation of viral entry into host cell / endosome membrane / viral protein processing / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. ...Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Galactose-binding domain-like / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
meta-guanidinomethyl-phenylacetyl-Arg-Val-Arg-(amidomethyl)benzamidine / Furin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDahms, S.O. / Arciniega, M. / Steinmetzer, T. / Huber, R. / Than, M.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism.
Authors: Dahms, S.O. / Arciniega, M. / Steinmetzer, T. / Huber, R. / Than, M.E.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Structure summary
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Dec 21, 2016Group: Non-polymer description
Revision 1.4Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 2.0Jul 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 6, 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: Furin
H: 2UC-ARG-VAL-ARG-00S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35410
Polymers53,1412
Non-polymers2138
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-56 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.080, 132.080, 155.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-604-

NA

21A-606-

NA

31A-1077-

HOH

41A-1103-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AH

#1: Protein Furin / Dibasic-processing enzyme / Paired basic amino acid residue-cleaving enzyme / PACE


Mass: 52388.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#2: Protein/peptide 2UC-ARG-VAL-ARG-00S


Type: Polypeptide / Class: Enzyme inhibitor / Mass: 751.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: meta-guanidinomethyl-phenylacetyl-Arg-Val-Arg-(amidomethyl)benzamidine

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Non-polymers , 4 types, 468 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→46.1 Å / Num. obs: 53880 / % possible obs: 98.9 % / Redundancy: 5 % / Rsym value: 0.136 / Net I/σ(I): 11.92
Reflection shellResolution: 2→2.12 Å / Rsym value: 0.788

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RYD

4ryd


Resolution: 2→43.233 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.21
RfactorNum. reflection% reflection
Rfree0.1889 2629 4.88 %
Rwork0.1668 --
obs0.1679 53866 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 8 460 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073811
X-RAY DIFFRACTIONf_angle_d1.0425196
X-RAY DIFFRACTIONf_dihedral_angle_d12.9041396
X-RAY DIFFRACTIONf_chiral_restr0.044561
X-RAY DIFFRACTIONf_plane_restr0.005694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.03680.27481330.25852592X-RAY DIFFRACTION97
2.0368-2.0760.2521320.23762668X-RAY DIFFRACTION99
2.076-2.11840.24151510.21332641X-RAY DIFFRACTION99
2.1184-2.16440.25991350.20832672X-RAY DIFFRACTION99
2.1644-2.21480.24961410.20412649X-RAY DIFFRACTION100
2.2148-2.27020.22991310.19472695X-RAY DIFFRACTION99
2.2702-2.33160.20441200.18562684X-RAY DIFFRACTION99
2.3316-2.40020.22881320.18242690X-RAY DIFFRACTION99
2.4002-2.47760.20471280.18122682X-RAY DIFFRACTION100
2.4776-2.56620.21511350.17962700X-RAY DIFFRACTION100
2.5662-2.66890.231200.1792714X-RAY DIFFRACTION100
2.6689-2.79030.20231490.17642705X-RAY DIFFRACTION99
2.7903-2.93740.1911420.17782684X-RAY DIFFRACTION99
2.9374-3.12140.17911360.1692683X-RAY DIFFRACTION99
3.1214-3.36230.17421500.1522716X-RAY DIFFRACTION99
3.3623-3.70050.15971520.13692728X-RAY DIFFRACTION99
3.7005-4.23560.14221440.122755X-RAY DIFFRACTION99
4.2356-5.33490.12991490.12752740X-RAY DIFFRACTION97
5.3349-43.24340.1891490.1732839X-RAY DIFFRACTION95

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