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

(-) Description

Title :  COORDINATES OF THE THERMUS THERMOPHILUS RIBOSOME BINDING FACTOR A (RBFA) HOMOLOGY MODEL AS FITTED INTO THE CRYO-EM MAP OF A 30S-RBFA COMPLEX
 
Authors :  P. P. Datta, D. N. Wilson, M. Kawazoe, N. K. Swami, T. Kaminishi, M. R. Sha T. M. Booth, C. Takemoto, P. Fucini, S. Yokoyama, R. K. Agrawal
Date :  22 Aug 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  12.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Helix-Kink-Helix, Kh Domain, Rrna Processing, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. P. Datta, D. N. Wilson, M. Kawazoe, N. K. Swami, T. Kaminishi, M. R. Sharma, T. M. Booth, C. Takemoto, P. Fucini, S. Yokoyama, R. K. Agrawal
Structural Aspects Of Rbfa Action During Small Ribosomal Subunit Assembly.
Mol. Cell V. 28 434 2007
PubMed-ID: 17996707  |  Reference-DOI: 10.1016/J.MOLCEL.2007.08.026

(-) Compounds

Molecule 1 - RIBOSOME-BINDING FACTOR A
    Chains: A
    Engineered: YES
    Gene: TTHA0907
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: RBFA, TTHA0907

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R1C)

(-) Sites  (0, 0)

(no "Site" information available for 2R1C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R1C)

(-) Exons   (0, 0)

(no "Exon" information available for 2R1C)

(-) 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:91
 aligned with RBFA_THET8 | Q5SJV1 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:91
                                    14        24        34        44        54        64        74        84        94 
            RBFA_THET8    5 KAHLEAQLKRALAEEIQALEDPRLFLLTVEAVRLSKDGSVLSVYVEAFREEEGALRALSRAERRLVAALARRVRMRRLPRLEFLPWRASPA 95
               SCOP domains d2r1ca1 A:5-94 Ribosome-binding factor A, RbfA                                            - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..........eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2r1c A  5 KAHLEAQLKRALAEEIQALEDPRLFLLTVEAVRLSKDGSVLSVYVEAFREEEGALRALSRAERRLVAALARRVRMRRLPRLEFLPWRASPA 95
                                    14        24        34        44        54        64        74        84        94
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R1C)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RBFA_THET8 | Q5SJV1)
biological process
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

 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
(no "Ligands, Modified Residues, Ions" information available for 2r1c)
 
  Sites
(no "Sites" information available for 2r1c)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r1c)
 

(-) 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 ](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
  2r1c
    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 (structure derived) | HSSP (homology derived)
    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
  RBFA_THET8 | Q5SJV1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  RBFA_THET8 | Q5SJV1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RBFA_THET8 | Q5SJV1: 2dyj

(-) Related Entries Specified in the PDB File

1jos
2dyj
2r1g RELATED ID: EMD-1413 RELATED DB: EMDB