Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A RIBOSWITCH-LIKE RNA-LIGAND COMPLEX FROM THE HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
 
Authors :  S. M. Dibrov, K. Ding, N. Brunn, M. A. Parker, B. M. Bergdahl, D. L. Wyles,
Date :  27 Sep 11  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Internal Loop, Regulatory Motif, Aminobenzimidazole Binding, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hermann, S. Dibrov, K. Ding, N. Brunn, M. Parker, M. Bergdahl, D. Wyles
Structure Of A Riboswitch In The Hepatitis C Virus Internal Ribosome Entry Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP *CP*C)-3'
    Chains: A
    Engineered: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Other Details: HCV IRES SUBDOMAIN IIA CHAIN A
    Synthetic: YES
 
Molecule 2 - 5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3'
    Chains: B
    Engineered: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Other Details: HCV IRES SUBDOMAIN IIA CHAIN B
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION
3SS01Ligand/Ion(8R)-8-[(DIMETHYLAMINO)METHYL]-1-[3-(DIMETHYLAMINO)PROPYL]-1,7,8,9-TETRAHYDROCHROMENO[5,6-D]IMIDAZOL-2-AMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREC A:55 , U A:56 , C A:58 , U A:59 , HOH A:80BINDING SITE FOR RESIDUE MG A 1
02AC2SOFTWAREG A:52 , U A:56 , A A:57 , MG A:69BINDING SITE FOR RESIDUE MG A 68
03AC3SOFTWAREHOH A:8 , U A:56 , C A:58 , C B:114 , G B:115BINDING SITE FOR RESIDUE MG B 1
04AC4SOFTWAREG A:52 , MG A:68 , SO4 A:73 , HOH A:87 , HOH B:69 , C B:112BINDING SITE FOR RESIDUE MG A 69
05AC5SOFTWAREA A:53 , SS0 A:75 , C B:108BINDING SITE FOR RESIDUE MG A 70
06AC6SOFTWAREA A:54 , HOH A:83 , HOH B:67 , G B:115BINDING SITE FOR RESIDUE MG A 71
07AC7SOFTWAREG A:49 , A A:50 , A A:54 , HOH A:79BINDING SITE FOR RESIDUE SO4 A 72
08AC8SOFTWAREG A:51 , G A:52 , MG A:69 , HOH B:69 , HOH B:70 , U B:113BINDING SITE FOR RESIDUE SO4 A 73
09AC9SOFTWAREC A:66 , C A:67 , HOH A:77 , HOH A:78BINDING SITE FOR RESIDUE SO4 A 74
10BC1SOFTWAREG A:52 , A A:53 , U A:56 , MG A:70 , HOH A:92 , HOH B:6 , A B:109 , G B:110 , C B:111BINDING SITE FOR RESIDUE SS0 A 75

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TZR)

(-) 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:RNA  Length:20
                                                    
                 3tzr A  48 CGAGGAACUACUGUCUUCCC  67
                                    57        67


Chain B from PDB  Type:RNA  Length:16
                                                
                 3tzr B 101 GGUCGUGCAGCCUCGG 116
                                   110
   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  (0, 0)

(no "SCOP Domain" information available for 3TZR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3TZR)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SS0  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tzr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tzr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP | HSSP
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3TZR)

(-) Related Entries Specified in the PDB File

2nok SAME RNA TARGET WITHOUT LIGAND