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- PDB-1dxw: structure of hetero complex of non structural protein (NS) of hep... -

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Basic information

Entry
Database: PDB / ID: 1dxw
Titlestructure of hetero complex of non structural protein (NS) of hepatitis C virus (HCV) and synthetic peptidic compound
ComponentsSERINE PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NON STRUCTURAL PROTEIN / HEPATITIS C VIRUS / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated transformation of host cell / host cell membrane / host cell mitochondrion / serine-type peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / host cell / channel activity / viral nucleocapsid ...host cell lipid droplet / symbiont-mediated transformation of host cell / host cell membrane / host cell mitochondrion / serine-type peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / host cell / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
BOC-GLU-LEU-FKI, PEPTIDE INHIBITOR / Chem-2ZF / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesHEPATITIS C VIRUS
MethodSOLUTION NMR / simulated annealing
AuthorsBarbato, G. / Cicero, D.O. / Cordier, F. / Narjes, F. / Gerlach, B. / Sambucini, S. / Grzesiek, S. / Matassa, V.G. / Defrancesco, R. / Bazzo, R.
Citation
Journal: Embo J. / Year: 2000
Title: Inhibitor Binding Induces Active Site Stabilisation of the Hcv Ns3 Protein Serine Protease Domain
Authors: Barbato, G. / Cicero, D.O. / Cordier, F. / Narjes, F. / Gerlach, B. / Sambucini, S. / Grzesiek, S. / Matassa, V.G. / Defrancesco, R. / Bazzo, R.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Solution Structure of the N-Terminal Serine Protease Domain of the Hepatitis C Virus Ns3 Protein Provides New Insights Into its Activation and Catalytic Mechanism
Authors: Barbato, G. / Cicero, D.O. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / Defrancesco, R. / Bazzo, R.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Structural Characterization of the Interactions of Optimized Product Inhibitors with the N-Terminal Proteinase Domain of the Hepatitis C Virus (Hcv) Ns3 Protein by NMR and Modelling Studies
Authors: Cicero, D.O. / Barbato, G. / Koch, U. / Ingallinella, P. / Bianchi, E. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / Matassa, V. / Defrancesco, R. / Pessi, A. / Bazzo, R.
#3: Journal: J.Biol.Chem. / Year: 1998
Title: The Metal Binding Site of the Hepatitis C Virus Ns3 Protease
Authors: Urbani, A. / Bazzo, R. / Nardi, M.C. / Cicero, D.O. / Defrancesco, R. / Steinkuhler, C. / Barbato, G.
History
DepositionJan 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jan 15, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_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.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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2093
Polymers19,6351
Non-polymers5752
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein SERINE PROTEASE / NS3


Mass: 19634.529 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 1027-1206
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN SER 139 OG AND ABK 190 C1 (DI-FLUORO-ABU-KETOACID) OF INHIBITOR
Source: (gene. exp.) HEPATITIS C VIRUS / Strain: BK / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P90191, UniProt: Q8QW30*PLUS
#2: Chemical ChemComp-2ZF / N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 509.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H33F2N3O9 / References: BOC-GLU-LEU-FKI, PEPTIDE INHIBITOR
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
Sequence details6 RESIDUES INSERTED AT THE C TERMINAL (ALA SER LYS LYS LYS LYS)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE EXPERIMENTS, 3D HETERONUCLEAR NOESY EXPERIMENTS, 3D AND 2D COUPLING CONSTANT MEASUREMENTS, 10% GLUCOSE C13 LABELLING FOR METHYL ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE EXPERIMENTS, 3D HETERONUCLEAR NOESY EXPERIMENTS, 3D AND 2D COUPLING CONSTANT MEASUREMENTS, 10% GLUCOSE C13 LABELLING FOR METHYL STEREOSPECIFIC ASSINGMENT, COMBINED USE OF SEVERAL COUPLING CONSTANTS AND ROESY SPECTROSCOPY TO DETERMINE CHI1 ANGLES.

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Sample preparation

DetailsContents: 95% WATER/10 % D2O
Sample conditionspH: 6.6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESIDUES OF NS3 1-21 ARE NOT INCLUDED IN THE MODELS SINCE THEY ARE AFFECTED BY MOBILITY IN SOLUTION.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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