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- PDB-6eqw: X-ray structure of the proprotein convertase furin bound with the... -

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Basic information

Entry
Database: PDB / ID: 6eqw
TitleX-ray structure of the proprotein convertase furin bound with the competitive inhibitor 4-aminomethyl-phenylacetyl-Arg-Val-Arg-Amba
Components
  • AMA-ARG-TBG-ARG-00S
  • Furin
KeywordsHYDROLASE / protease / inhibitor / proprotein convertase
Function / homology
Function and homology information


furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / peptide biosynthetic process / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / peptide biosynthetic process / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / secretion by cell / Synthesis and processing of ENV and VPU / nerve growth factor binding / Formation of the cornified envelope / Signaling by PDGF / trans-Golgi network transport vesicle / blastocyst formation / Elastic fibre formation / heparan sulfate binding / Signaling by NODAL / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / regulation of endopeptidase activity / peptide hormone processing / CD163 mediating an anti-inflammatory response / regulation of protein catabolic process / Activation of Matrix Metalloproteinases / TGF-beta receptor signaling activates SMADs / Uptake and function of anthrax toxins / protein maturation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / regulation of signal transduction / Removal of aminoterminal propeptides from gamma-carboxylated proteins / viral life cycle / negative regulation of inflammatory response to antigenic stimulus / serine-type peptidase activity / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / serine-type endopeptidase inhibitor activity / protein processing / Golgi lumen / heparin binding / peptidase activity / viral translation / endopeptidase activity / Induction of Cell-Cell Fusion / protease binding / amyloid fibril formation / Potential therapeutics for SARS / Attachment and Entry / positive regulation of viral entry into host cell / viral protein processing / endosome membrane / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / metal ion binding / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Galactose-binding domain-like / Furin-like repeat / Furin-like repeats / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsDahms, S.O. / Than, M.E.
CitationJournal: Biochemistry / Year: 2018
Title: X-ray Structures of the Proprotein Convertase Furin Bound with Substrate Analogue Inhibitors Reveal Substrate Specificity Determinants beyond the S4 Pocket.
Authors: Dahms, S.O. / Hardes, K. / Steinmetzer, T. / Than, M.E.
History
DepositionOct 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin
D: AMA-ARG-TBG-ARG-00S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,36010
Polymers53,1132
Non-polymers2488
Water8,755486
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-62 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.713, 131.713, 155.393
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-607-

NA

31A-1105-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#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 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin
#2: Protein/peptide AMA-ARG-TBG-ARG-00S


Mass: 723.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 494 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 486 / 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

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NaH2PO4, PH 5.5-6.0, 3-4 M NaCL, 3% DMSO; RESERVOIR SOLUTION: 3-4M 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: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.99→46 Å / Num. obs: 54283 / % possible obs: 99.3 % / Redundancy: 6.57 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.14 / Net I/σ(I): 13.48
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 8600 / CC1/2: 0.829 / Rrim(I) all: 0.808 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JXH
Resolution: 1.994→45.976 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.6
RfactorNum. reflection% reflection
Rfree0.1842 2657 4.9 %
Rwork0.1619 --
obs0.163 54274 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.994→45.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 8 486 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063780
X-RAY DIFFRACTIONf_angle_d0.8265158
X-RAY DIFFRACTIONf_dihedral_angle_d21.432254
X-RAY DIFFRACTIONf_chiral_restr0.054559
X-RAY DIFFRACTIONf_plane_restr0.005685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9939-2.03020.24951380.22742631X-RAY DIFFRACTION98
2.0302-2.06920.23641360.21522673X-RAY DIFFRACTION100
2.0692-2.11150.25581520.19832675X-RAY DIFFRACTION100
2.1115-2.15740.22121340.19182689X-RAY DIFFRACTION100
2.1574-2.20760.2331380.18512674X-RAY DIFFRACTION100
2.2076-2.26280.20441330.17762713X-RAY DIFFRACTION100
2.2628-2.3240.24141230.17982691X-RAY DIFFRACTION100
2.324-2.39230.1941320.16592716X-RAY DIFFRACTION100
2.3923-2.46950.19421300.17972691X-RAY DIFFRACTION100
2.4695-2.55780.21661340.1792714X-RAY DIFFRACTION100
2.5578-2.66020.20411230.17212719X-RAY DIFFRACTION100
2.6602-2.78130.19181510.17032702X-RAY DIFFRACTION100
2.7813-2.92790.1971430.17172729X-RAY DIFFRACTION100
2.9279-3.11130.16851380.16472706X-RAY DIFFRACTION99
3.1113-3.35140.1761510.14962725X-RAY DIFFRACTION99
3.3514-3.68860.16271500.13972733X-RAY DIFFRACTION99
3.6886-4.2220.15091450.12532754X-RAY DIFFRACTION99
4.222-5.3180.14251500.12632797X-RAY DIFFRACTION99
5.318-45.98840.17141560.17632885X-RAY DIFFRACTION96

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