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(-) Description

Title :  CRYSTAL STRUCTURE OF ALFALFA MOSAIC VIRUS RNA 3'UTR IN COMPLEX WITH COAT PROTEIN N TERMINAL PEPTIDE
 
Authors :  L. M. Guogas, D. J. Filman, J. M. Hogle, L. Gehrke
Date :  06 Oct 04  (Deposition) - 04 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Rna Complex, Alpha Helix, Atypical Rna Duplex, Viral Protein- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Guogas, D. J. Filman, J. M. Hogle, L. Gehrke
Cofolding Organizes Alfalfa Mosaic Virus Rna And Coat Protein For Replication.
Science V. 306 2108 2004
PubMed-ID: 15604410  |  Reference-DOI: 10.1126/SCIENCE.1103399

(-) Compounds

Molecule 1 - ALFALFA MOSAIC VIRUS RNA 3' UTR
    Chains: A
    Engineered: YES
    Fragment: AMV RNA BASES 843-872
    Other Details: RNA SYNTHESIS DHARMACON RESEARCH
    Synthetic: YES
 
Molecule 2 - ALFALFA MOSAIC VIRUS RNA 3' UTR
    Chains: B
    Engineered: YES
    Fragment: AMV RNA BASES 873-881
    Other Details: RNA SYNTHESIS DHARMACON RESEARCH
    Synthetic: YES
 
Molecule 3 - COAT PROTEIN
    Chains: C, D
    Engineered: YES
    Fragment: AMV COAT PROTEIN RESIDUES 1-26
    Other Details: PEPTIDE SYNTHESIS BY MIT BIOPOLYMERS LABORATORY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BR1Ligand/IonBROMIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:871 , U A:872BINDING SITE FOR RESIDUE BR A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XOK)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:27
                                                           
                 1xok A 843 AUGCUCAUGCACUGCAUGAAUGCCCCU 872
                                   852|      865       
                                   852|                
                                    856                


Chain B from PDB  Type:RNA  Length:9
                                         
                 1xok B 873 AAGGGAUGC 881


Chain C from PDB  Type:PROTEIN  Length:15
 aligned with CAPSD_AMVYS | P24264 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:15
                                    22     
          CAPSD_AMVYS    13 GKPTKRSQNYAALRK  27
               SCOP domains d1xokc_ C:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1xok C  12 GKPTKRSQNYAALRK  26
                                    21     


Chain D from PDB  Type:PROTEIN  Length:18
 aligned with CAPSD_AMVYS | P24264 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:18
                                    19        
          CAPSD_AMVYS    10 GKAGKPTKRSQNYAALRK  27
               SCOP domains d1xokd_ D:         SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 1xok D   9 GKAGKPTKRSQNYAALRK  26
                                    18
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (CAPSD_AMVYS | P24264)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
    GO:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    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:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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