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(-) Description

Title :  STRUCTURE OF A VIRAL OTU DOMAIN PROTEASE BOUND TO INTERFERON-STIMULATED GENE 15 (ISG15)
 
Authors :  J. P. Bacik, T. W. James, N. Frias-Staheli, A. Garcia-Sastre, B. L. Mark
Date :  01 Dec 10  (Deposition) - 19 Jan 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Deubiquitinase, 3-Aminopropane, Intein-Mediated Ligation, Crimean-Congo Hemorrhagic Fever Virus, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. W. James, N. Frias-Staheli, J. P. Bacik, J. M. Levingston Macleod, M. Khajehpour, A. Garcia-Sastre, B. L. Mark
Structural Basis For The Removal Of Ubiquitin And Interferon-Stimulated Gene 15 By A Viral Ovarian Tumor Domain-Containing Protease.
Proc. Natl. Acad. Sci. Usa V. 108 2222 2011
PubMed-ID: 21245344  |  Reference-DOI: 10.1073/PNAS.1013388108

(-) Compounds

Molecule 1 - RNA POLYMERASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentOTU DOMAIN (UNP RESIDUES 1-169)
    Organism ScientificCRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
    Organism Taxid11593
 
Molecule 2 - UBIQUITIN-LIKE PROTEIN ISG15
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneISG15, G1P2, UCRP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINTERFERON-INDUCED 15 KDA PROTEIN, INTERFERON-INDUCED 17 KDA PROTEIN, IP17, UBIQUITIN CROSS-REACTIVE PROTEIN, HUCRP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13CN1Ligand/Ion3-AMINOPROPANE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:37 , CYS A:40 , TRP A:99 , THR A:150 , HIS A:151 , GLY B:156BINDING SITE FOR RESIDUE 3CN B 157
2AC2SOFTWAREASN A:20 , ARG B:87 , ASN B:88 , ASN B:89 , GLY B:91 , MET B:150 , HOH B:184BINDING SITE FOR RESIDUE GOL B 1344

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His B:48 -Pro B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016181S83NISG15_HUMANPolymorphism1921BN83N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.ISG15_HUMAN3-80
82-157
  1-
B:82-156

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003793891ENSE00001480807chr1:948803-948956154ISG15_HUMAN1-110--
1.2ENST000003793892ENSE00001480799chr1:949364-949920557ISG15_HUMAN2-1651641B:4-156 (gaps)153

(-) 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:164
 aligned with Q6TQF5_9VIRU | Q6TQF5 from UniProtKB/TrEMBL  Length:3945

    Alignment length:164
                              1                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    
         Q6TQF5_9VIRU     - --MDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------OTU-3pseA01 A:35-152                                                                                                  ---------- Pfam domains
         Sec.struct. author ...hhhh....eeee..eeee.....hhh.eeee.......hhhhhhhhhh.......hhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhh.......hhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeeeee...eeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pse A  -1 GPMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with ISG15_HUMAN | P05161 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:153
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153   
          ISG15_HUMAN     4 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKCDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 156
               SCOP domains d3pseb1 B:4-78 a   utomated matches                                        d3pseb2 B:79-156 automated matches                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------ubiquitin-3pseB01 B:87-155                                           - Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------ubiquitin-3pseB02 B:87-155                                           - Pfam domains (2)
         Sec.struct. author eeeeee....eeeee.---..hhhhhhhhhhhh..hhhheeeee...........hhhh.......eeeeee......eeeeee.....eeeeee.....hhhhhhhhhhhh..hhhheeee...........hhhh......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------N------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: - UniProt: 3-80                                            -UBIQUITIN_2  PDB: B:82-156 UniProt: 82-157                                  PROSITE
               Transcript 1 Exon 1.2  PDB: B:4-156 (gaps) UniProt: 2-165 [INCOMPLETE]                                                                                                 Transcript 1
                 3pse B   4 DLTVKMLAGNEFQVSL---MSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLNILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 156
                                    13     |  23        33        43        53        63        73        83        93       103       113       123       133       143       153   
                                          19  23                                                                                                                                     

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6TQF5_9VIRU | Q6TQF5)
molecular function
    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: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: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.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.

Chain B   (ISG15_HUMAN | P05161)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0032020    ISG15-protein conjugation    The covalent addition to a protein of ISG15, a ubiquitin-like protein.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0019941    modification-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0032649    regulation of interferon-gamma production    Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0034340    response to type I interferon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ISG15_HUMAN | P051611z2m 2hj8 3phx 3r66 3rt3 3sdl 5tl6
UniProtKB/TrEMBL
        Q6TQF5_9VIRU | Q6TQF53pt2

(-) Related Entries Specified in the PDB File

3pt2 VIRAL OTU DOMAIN PROTEASE BOUND TO UBIQUITIN