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- PDB-5jmo: X-ray structure of furin in complex with the inhibitory antibody Nb14 -

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Basic information

Entry
Database: PDB / ID: 5jmo
TitleX-ray structure of furin in complex with the inhibitory antibody Nb14
Components
  • CMK-inhibitor
  • Furin
  • camelid VHH fragment
KeywordsHydrolase/Antibody / protease / camelid / antibody / complex / Hydrolase-Antibody complex / furin
Function / homology
Function and homology information


furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / regulation of endopeptidase activity / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / signal peptide processing / regulation of cholesterol transport ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / regulation of endopeptidase activity / negative regulation of transforming growth factor beta1 production / Assembly of active LPL and LIPC lipase complexes / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / cytokine precursor processing / secretion by cell / Pre-NOTCH Processing in Golgi / Synthesis and processing of ENV and VPU / nerve growth factor binding / Formation of the cornified envelope / symbiont-mediated induction of syncytium formation / Signaling by PDGF / trans-Golgi network transport vesicle / Signaling by NODAL / heparan sulfate binding / blastocyst formation / Elastic fibre formation / peptide hormone processing / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / CD163 mediating an anti-inflammatory response / Activation of Matrix Metalloproteinases / Maturation of hRSV A proteins / regulation of protein catabolic process / TGF-beta receptor signaling activates SMADs / Collagen degradation / Uptake and function of anthrax toxins / Respiratory syncytial virus (RSV) attachment and entry / collagen catabolic process / extracellular matrix disassembly / regulation of signal transduction / Removal of aminoterminal propeptides from gamma-carboxylated proteins / viral life cycle / extracellular matrix organization / serine-type peptidase activity / transforming growth factor beta receptor signaling pathway / protein maturation / peptide binding / negative regulation of inflammatory response to antigenic stimulus / trans-Golgi network / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / protein processing / Golgi lumen / peptidase activity / heparin binding / protease binding / endopeptidase activity / viral translation / amyloid fibril formation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE / Furin
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus dromedarius (Arabian camel)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsDahms, S.O. / Than, M.E.
CitationJournal: Sci Rep / Year: 2016
Title: The structure of a furin-antibody complex explains non-competitive inhibition by steric exclusion of substrate conformers.
Authors: Dahms, S.O. / Creemers, J.W. / Schaub, Y. / Bourenkov, G.P. / Zogg, T. / Brandstetter, H. / Than, M.E.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Non-polymer description
Revision 1.2Jan 11, 2017Group: Structure summary
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.pdbx_role / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin
B: Furin
C: camelid VHH fragment
D: camelid VHH fragment
G: CMK-inhibitor
H: CMK-inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,67718
Polymers131,5066
Non-polymers1,17112
Water13,854769
1
A: Furin
C: camelid VHH fragment
G: CMK-inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3399
Polymers65,7533
Non-polymers5866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-32 kcal/mol
Surface area22290 Å2
MethodPISA
2
B: Furin
D: camelid VHH fragment
H: CMK-inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3399
Polymers65,7533
Non-polymers5866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-33 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.775, 50.039, 144.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-969-

HOH

21B-1027-

HOH

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 10 molecules ABCDGH

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


Mass: 52388.602 Da / Num. of mol.: 2
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: Antibody camelid VHH fragment


Mass: 12615.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide CMK-inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 749.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 777 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#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


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: .1 M sodium acetate, pH 5.6, 16-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.998→66.381 Å / Num. obs: 83341 / % possible obs: 98.8 % / Redundancy: 6.73 % / Rsym value: 0.132 / Net I/σ(I): 12.02
Reflection shellResolution: 1.998→2.12 Å / Rsym value: 0.608

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RYD (furin, chain A or chain B) and 5JMR (antibody, chain C or chain D)

4ryd

5jmr


Resolution: 1.998→66.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 4181 5.02 %
Rwork0.163 --
obs0.1647 83298 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→66.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9025 0 64 769 9858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079353
X-RAY DIFFRACTIONf_angle_d1.05412736
X-RAY DIFFRACTIONf_dihedral_angle_d13.5893390
X-RAY DIFFRACTIONf_chiral_restr0.0431389
X-RAY DIFFRACTIONf_plane_restr0.0071673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9979-2.020700.2072517X-RAY DIFFRACTION91
2.0207-2.04440.24582790.19642455X-RAY DIFFRACTION100
2.0444-2.069400.19222739X-RAY DIFFRACTION98
2.0694-2.09560.24762790.18912440X-RAY DIFFRACTION97
2.0956-2.123100.17762746X-RAY DIFFRACTION100
2.1231-2.15220.21642790.18522484X-RAY DIFFRACTION99
2.1522-2.18300.18052716X-RAY DIFFRACTION96
2.183-2.21560.22242790.1722446X-RAY DIFFRACTION100
2.2156-2.250200.17212760X-RAY DIFFRACTION99
2.2502-2.28710.21342790.17732431X-RAY DIFFRACTION97
2.2871-2.326500.17372754X-RAY DIFFRACTION100
2.3265-2.36880.22182780.17722503X-RAY DIFFRACTION99
2.3688-2.414400.1742724X-RAY DIFFRACTION98
2.4144-2.46370.24442790.17152522X-RAY DIFFRACTION100
2.4637-2.517200.17182735X-RAY DIFFRACTION98
2.5172-2.57580.19172780.16222484X-RAY DIFFRACTION100
2.5758-2.640200.1722774X-RAY DIFFRACTION98
2.6402-2.71160.21092790.16882501X-RAY DIFFRACTION100
2.7116-2.791400.16922752X-RAY DIFFRACTION97
2.7914-2.88150.20042790.17322512X-RAY DIFFRACTION100
2.8815-2.984500.16132783X-RAY DIFFRACTION99
2.9845-3.1040.20462790.16952538X-RAY DIFFRACTION100
3.104-3.245200.16792754X-RAY DIFFRACTION98
3.2452-3.41630.19322790.16462522X-RAY DIFFRACTION99
3.4163-3.630300.16142829X-RAY DIFFRACTION99
3.6303-3.91060.17432780.14952568X-RAY DIFFRACTION100
3.9106-4.304100.1262838X-RAY DIFFRACTION100
4.3041-4.92670.14212780.12762616X-RAY DIFFRACTION100
4.9267-6.206500.1482915X-RAY DIFFRACTION100
6.2065-66.41730.20582790.17342759X-RAY DIFFRACTION99

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