[English] 日本語
Yorodumi
- PDB-1dxw: structure of hetero complex of non structural protein (NS) of hep... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / symbiont entry into host cell / 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 / Trypsin-like serine proteases / Helicase superfamily 1/2, ATP-binding domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
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.

-
Sample preparation

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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more