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(-) Description

Title :  CRYSTAL STRUCTURE OF NS3/4A PROTEASE VARIANT D168A IN COMPLEX WITH DANOPREVIR
 
Authors :  C. A. Schiffer, K. P. Romano
Date :  11 Jul 11  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Ns3, Drug Resistance, Drug Design, Protease Inhibitors, Hcv, Serine Protease, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. P. Romano, A. Ali, C. Aydin, D. Soumana, A. Ozen, L. M. Deveau, C. Silver, H. Cao, A. Newton, C. J. Petropoulos, W. Huang, C. A. Schiffe
The Molecular Basis Of Drug Resistance Against Hepatitis C Virus Ns3/4A Protease Inhibitors.
Plos Pathog. V. 8 02832 2012
PubMed-ID: 22910833  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002832

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNS3-NS4A
    Organism ScientificHEPATITIS C VIRUS SUBTYPE 1A
    Organism Taxid31646
    StrainBID-V318

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2TSV1Ligand/Ion(2R,6S,12Z,13AS,14AR,16AS)-6-[(TERT-BUTOXYCARBONYL)AMINO]-14A-[(CYCLOPROPYLSULFONYL)CARBAMOYL]-5,16-DIOXO-1,2,3,5,6,7,8,9,10,11,13A,14,14A,15,16,16A-HEXADECAHYDROCYCLOPROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECIN-2-YL 4-FLUORO-2H-ISOINDOLE-2-CARBOXYLATE
3ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:56 , HOH A:155 , HOH A:161 , HOH A:166 , HIS A:982 , GLN A:1041 , PHE A:1043 , HIS A:1057 , GLY A:1058 , ASP A:1079 , ASP A:1081 , ARG A:1123 , LEU A:1135 , LYS A:1136 , GLY A:1137 , SER A:1138 , ALA A:1139 , PHE A:1154 , ARG A:1155 , ALA A:1156 , ALA A:1157BINDING SITE FOR RESIDUE TSV A 100
2AC2SOFTWAREHOH A:11 , HOH A:13 , HOH A:57 , HOH A:64 , HOH A:140 , TYR A:1006 , GLN A:1008 , TYR A:1056BINDING SITE FOR RESIDUE SO4 A 1
3AC3SOFTWAREHOH A:93 , HOH A:133 , HOH A:196 , LYS A:1080 , ARG A:1155 , PRO A:1171 , SER A:1174BINDING SITE FOR RESIDUE SO4 A 2
4AC4SOFTWAREHOH A:74 , HOH A:120 , HOH A:175 , ARG A:1109 , HIS A:1110BINDING SITE FOR RESIDUE SO4 A 4
5AC5SOFTWAREHOH A:198 , SER A:1122 , ARG A:1123 , ARG A:1155 , ALA A:1168BINDING SITE FOR RESIDUE SO4 A 5
6AC6SOFTWARECYS A:1097 , CYS A:1099 , CYS A:1145 , HIS A:1149BINDING SITE FOR RESIDUE ZN A 1183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SU1)

(-) Exons   (0, 0)

(no "Exon" information available for 3SU1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:200
 aligned with A8DG50_9HEPC | A8DG50 from UniProtKB/TrEMBL  Length:3011

    Alignment length:256
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      
        A8DG50_9HEPC    951 NHLTPLRDWAHNGLQDLAVAVEPVVFSPMETKLITWGADTAACGDIINGLPVSARRGQEILLGPADGVVSKGWRLLAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVESLETTMR 1206
               SCOP domains d3su1a_                                                A: automate         d matches                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.-----------------------------------------------.....eeeeeee---------......eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeee.hhh......eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3su1 A  981 SHMASMK-----------------------------------------------KKGSVVIVGRIN---------LSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSAGGPLLCPAGHAVGIFRAAVSTRGVAKAVAFIPVESLETTMR 1180
                                  |  -         -         -         -         -    |  993     |   -     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      
                                987                                             988        999      1000                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SU1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SU1)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A8DG50_9HEPC | A8DG50)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019087    transformation of host cell by virus    Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        A8DG50_9HEPC | A8DG505voj 5vp9
UniProtKB/TrEMBL
        A8DG50_9HEPC | A8DG503m5l 3m5m 3m5n 3m5o 3rc6 3su0 3su2 3su3 3su4 3su5 3su6 3sud 3sue 3suf 3sug 3sv6 3sv7 3sv8 3sv9 4nwk 4nwl 4wh6 4wh8

(-) Related Entries Specified in the PDB File

3ssn 3su0 3su1 3su2 3su3 3su4 3su5 3su6 3sud 3sue 3suf 3sug 3sv6 3sv7 3sv8 3sv9 3syt 3sz0 3szc 3szf 3szg 3szw 3t0k