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(-) Description

Title :  RECOGNITION OF THE ROTAVIRUS MRNA 3' CONSENSUS BY AN ASYMMETRIC NSP3 HOMODIMER
 
Authors :  R. C. Deo, C. M. Groft, K. R. Rajashankar, S. K. Burley
Date :  19 Dec 01  (Deposition) - 17 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,I,J,M,N,W,X,Y,Z
Biol. Unit 1:  A,B,W  (1x)
Biol. Unit 2:  C,D,X  (1x)
Biol. Unit 3:  I,J,Y  (1x)
Biol. Unit 4:  M,N,Z  (1x)
Keywords :  Protein-Ssrna Complex, Viral Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Deo, C. M. Groft, K. R. Rajashankar, S. K. Burley
Recognition Of The Rotavirus Mrna 3' Consensus By An Asymmetric Nsp3 Homodimer.
Cell(Cambridge, Mass. ) V. 108 71 2002
PubMed-ID: 11792322  |  Reference-DOI: 10.1016/S0092-8674(01)00632-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*GP*AP*CP*C)-3'
    ChainsW, X, Y, Z
    EngineeredYES
    SyntheticYES
 
Molecule 2 - NONSTRUCTURAL RNA-BINDING PROTEIN 34
    ChainsA, B, C, D, I, J, M, N
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    Organism ScientificSIMIAN ROTAVIRUS A/SA11
    Organism Taxid10923
    StrainSA-11
    SynonymNS34, NSP3

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDIJMNWXYZ
Biological Unit 1 (1x)AB      W   
Biological Unit 2 (1x)  CD     X  
Biological Unit 3 (1x)    IJ    Y 
Biological Unit 4 (1x)      MN   Z

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KNZ)

(-) Sites  (0, 0)

(no "Site" information available for 1KNZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KNZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KNZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KNZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KNZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1KNZ)

(-) Sequences/Alignments

Asymmetric 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:154
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           NSP3_ROTS1     7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
               SCOP domains d1knza_ A: NSP3 homodimer                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh---.hhhhhhhhhhhheee........eee.hhhhhhhhh...eeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz A   7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMML---GIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
                                    16        26        36        46        56        66        76        86        96       106 |   | 116       126       136       146       156       
                                                                                                                               108 112                                                   

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NSP3_ROTS1     2 LKMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
               SCOP domains d1knzb_ B: NSP3 homodimer                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh--------------..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhheeee......eeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz B   2 GSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALN--------------DTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
                                    11        21        31        41        51        61        71   |     -        91       101       111       121       131       141       151  
                                                                                                    75             90                                                               

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           NSP3_ROTS1     7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
               SCOP domains d1knzc_ C: NSP3 homodimer                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh---.hhhhhhhhhh..eee........eee.hhhhhhhhh...ee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz C   7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMML---GIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
                                    16        26        36        46        56        66        76        86        96       106 |   | 116       126       136       146       156       
                                                                                                                               108 112                                                   

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NSP3_ROTS1     2 LKMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
               SCOP domains d1knzd_ D: NSP3 homodimer                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh--------------..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhheeee........eeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz D   2 GSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALN--------------DTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
                                    11        21        31        41        51        61        71   |     -        91       101       111       121       131       141       151  
                                                                                                    75             90                                                               

Chain I from PDB  Type:PROTEIN  Length:154
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           NSP3_ROTS1     7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
               SCOP domains d1knzi_ I: NSP3 homodimer                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh---.hhhhhhhhhhhheee........eee.hhhhhhhhh...ee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz I   7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMML---GIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
                                    16        26        36        46        56        66        76        86        96       106 |   | 116       126       136       146       156       
                                                                                                                               108 112                                                   

Chain J from PDB  Type:PROTEIN  Length:138
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NSP3_ROTS1     2 LKMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
               SCOP domains d1knzj_ J: NSP3 homodimer                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh--------------..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhheeee........eeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz J   2 GSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALN--------------DTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
                                    11        21        31        41        51        61        71   |     -        91       101       111       121       131       141       151  
                                                                                                    75             90                                                               

Chain M from PDB  Type:PROTEIN  Length:154
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           NSP3_ROTS1     7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
               SCOP domains d1knzm_ M: NSP3 homodimer                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh---.hhhhhhhhhh..eee........eee.hhhhhhhhh...ee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz M   7 TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMML---GIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKM 163
                                    16        26        36        46        56        66        76        86        96       106 |   | 116       126       136       146       156       
                                                                                                                               108 112                                                   

Chain N from PDB  Type:PROTEIN  Length:138
 aligned with NSP3_ROTS1 | P03536 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           NSP3_ROTS1     2 LKMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
               SCOP domains d1knzn_ N: NSP3 homodimer                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh--------------..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhheeee........eeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knz N   2 GSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALN--------------DTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVE 153
                                    11        21        31        41        51        61        71   |     -        91       101       111       121       131       141       151  
                                                                                                    75             90                                                               

Chain W from PDB  Type:RNA  Length:5
                                     
                 1knz W   2 UGACC   6

Chain X from PDB  Type:RNA  Length:5
                                     
                 1knz X   2 UGACC   6

Chain Y from PDB  Type:RNA  Length:5
                                     
                 1knz Y   2 UGACC   6

Chain Z from PDB  Type:RNA  Length:5
                                     
                 1knz Z   2 UGACC   6

   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, 8)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KNZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KNZ)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,I,J,M,N   (NSP3_ROTS1 | P03536)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NSP3_ROTS1 | P035361lj2

(-) Related Entries Specified in the PDB File

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