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- PDB-5jxh: Structure the proprotein convertase furin in complex with meta-gu... -

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Basic information

Entry
Database: PDB / ID: 5jxh
TitleStructure the proprotein convertase furin in complex with meta-guanidinomethyl-Phac-RVR-Amba at 2.0 Angstrom resolution.
Components
  • 2UC-ARG-VAL-ARG-00S
  • Furin
KeywordsHYDROLASE / protease / inhibitor / proteolysis / hydrolase
Function / homology
Function and homology information


Signaling by PDGF / Amyloid fiber formation / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Uptake and function of anthrax toxins / TGF-beta receptor signaling activates SMADs / Signaling by NODAL / Pre-NOTCH Processing in Golgi / Synthesis and processing of ENV and VPU / NGF processing ...Signaling by PDGF / Amyloid fiber formation / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Uptake and function of anthrax toxins / TGF-beta receptor signaling activates SMADs / Signaling by NODAL / Pre-NOTCH Processing in Golgi / Synthesis and processing of ENV and VPU / NGF processing / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Activation of Matrix Metalloproteinases / Elastic fibre formation / Collagen degradation / zymogen inhibition / positive regulation of transforming growth factor beta1 activation / dibasic protein processing / furin / nerve growth factor production / regulation of lipoprotein lipase activity / nerve growth factor processing / regulation of low-density lipoprotein particle receptor biosynthetic process / negative regulation of low-density lipoprotein particle receptor catabolic process / signal peptide processing / negative regulation of transforming growth factor beta1 production / peptide biosynthetic process / peptide hormone processing / secretion by cell / integral component of Golgi membrane / nerve growth factor binding / cornification / trans-Golgi network transport vesicle / regulation of endopeptidase activity / zymogen activation / positive regulation of membrane protein ectodomain proteolysis / regulation of protein catabolic process / regulation of signal transduction / protein processing / collagen catabolic process / extracellular matrix disassembly / peptide binding / viral protein processing / trans-Golgi network / viral life cycle / serine-type endopeptidase inhibitor activity / transforming growth factor beta receptor signaling pathway / Golgi lumen / extracellular matrix organization / peptidase activity / endopeptidase activity / endosome membrane / protease binding / membrane raft / Golgi membrane / serine-type endopeptidase activity / cellular protein metabolic process / endoplasmic reticulum / cell surface / extracellular exosome / membrane / extracellular region / plasma membrane / metal ion binding
Growth factor receptor cysteine-rich domain superfamily / Peptidase S8, pro-domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Peptidase S8, pro-domain superfamily / Peptidase S8, subtilisin, Asp-active site / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin-related / Subtilase family / Proprotein convertase P-domain ...Growth factor receptor cysteine-rich domain superfamily / Peptidase S8, pro-domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Peptidase S8, pro-domain superfamily / Peptidase S8, subtilisin, Asp-active site / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin-related / Subtilase family / Proprotein convertase P-domain / Peptidase S8/S53 domain / P domain / Peptidase S8 pro-domain / Serine proteases, subtilase family, aspartic acid active site. / Serine proteases, subtilase family, histidine active site. / Furin-like repeat / Serine proteases, subtilase family, serine active site. / P/Homo B domain profile. / Galactose-binding-like domain superfamily / Kexin/furin catalytic domain
Furin
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 13, 2016 / Release: Oct 5, 2016
RevisionDateData content typeGroupProviderType
1.0Oct 5, 2016Structure modelrepositoryInitial release
1.1Oct 12, 2016Structure modelStructure summary
1.2Oct 19, 2016Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Furin
H: 2UC-ARG-VAL-ARG-00S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,37210
Polymers53,1252
Non-polymers2488
Water9,620534
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-65 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)131.790, 131.790, 155.578
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-606-

NA

21A-1127-

HOH

31A-1159-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules AH

#1: Protein/peptide 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 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#2: Protein/peptide 2UC-ARG-VAL-ARG-00S


Mass: 735.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

about BIRD dictionary

PRD-IDPRD_001220
ClassEnzyme inhibitor
Namemeta-guanidinomethyl-phenylacetyl-Arg-Val-Arg-(amidomethyl)benzamidine
TypePolypeptidePeptide

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Non-polymers , 4 types, 542 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Calcium
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Sodium
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.67 Å3/Da / Density % sol: 66.49 %
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 PILATUS3 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→43.138 Å / Num. obs: 53872 / % possible obs: 99.2 % / Redundancy: 4.9 % / Rsym value: 0.108 / Net I/σ(I): 13.48
Reflection shellResolution: 2→2.12 Å / Rsym value: 0.575

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RYD
Resolution: 2→43.138 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.34
RfactorNum. reflection% reflection
Rfree0.1853 2632 4.89 %
Rwork0.1566 --
Obs0.158 53838 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 8 534 4204
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0073814
f_angle_d1.0425200
f_dihedral_angle_d13.2781398
f_chiral_restr0.042561
f_plane_restr0.005695
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03640.2471350.2186262699
2.0364-2.07560.23661310.206264599
2.0756-2.11790.23281510.1943261599
2.1179-2.1640.24621350.1864264999
2.164-2.21430.22521360.1762267099
2.2143-2.26970.21981320.1742263999
2.2697-2.33110.19341180.17264698
2.3311-2.39970.20621280.1641269799
2.3997-2.47710.17921310.1705266099
2.4771-2.56560.19621280.16682690100
2.5656-2.66830.20721260.16782684100
2.6683-2.78980.19881490.1672702100
2.7898-2.93680.22431440.1682697100
2.9368-3.12080.1631340.16372705100
3.1208-3.36160.17811530.1494267798
3.3616-3.69970.1751480.13052722100
3.6997-4.23470.14431470.11812756100
4.2347-5.33370.14311480.12342789100
5.3337-43.14840.17681580.1667293799

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