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 :  STRUCTURE DETERMINATION OF FIBRILLARIN HOMOLOGUE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS (PFU-65527)
 
Authors :  L. Deng, N. G. Starostina, Z. -J. Liu, J. P. Rose, R. M. Terns, M. P. Terns, B. -C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  20 Jun 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Fibrillarin, Pyrococcus Furiosus, Snornp, Ribosomal Rna Processing, Methylation, Pfu-65527, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Deng, N. G. Starostina, Z. -J. Liu, J. P. Rose, R. M. Terns, M. P. Terns, B. -C. Wang, Southeast Collaboratory For Structural Genomics
Structure Determination Of Fibrillarin From The Hyperthermophilic Archaeon Pyrococcus Furiosus
Biochem. Biophys. Res. Commun. V. 315 726 2004
PubMed-ID: 14975761  |  Reference-DOI: 10.1016/J.BBRC.2004.01.114
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-21B(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: FLPA OR PF0059
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 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 1PRY)

(-) Sites  (0, 0)

(no "Site" information available for 1PRY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRILLARINPS00566 Fibrillarin signature.FLPA_PYRFU99-113  1A:99-113

(-) Exons   (0, 0)

(no "Exon" information available for 1PRY)

(-) 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:226
 aligned with FLPA_PYRFU | Q8U4M2 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           FLPA_PYRFU     2 VEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP 227
               SCOP domains d1prya_ A: Fibrillarin homologue                                                                                                                                                                                                   SCOP domains
               CATH domains 1pryA01 A:2-51 Phosphorylase Kinase; domain 1     1pryA02 A:52-227 Vaccinia Virus protein VP39                                                                                                                                     CATH domains
               Pfam domains --Fibrillarin-1pryA01 A:4-227                                                                                                                                                                                                      Pfam domains
         Sec.struct. author .eeee.....eeeee.....eeeeee............eeee..eeeee.....hhhhhhhhh...........eeeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhhhhh..eeeeee.....hhhhhhhhhhhhheeeeeeeeeeeehhhhh...hhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------FIBRILLARIN    ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pry A   2 VEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERLLSEYFEVIERLNLEPYEKDHALFVVRKP 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FLPA_PYRFU | Q8U4M2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

 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 1pry)
 
  Sites
(no "Sites" information available for 1pry)
 
  Cis Peptide Bonds
    Glu A:213 - Pro A:214   [ RasMol ]  
 

(-) 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
  1pry
    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
  FLPA_PYRFU | Q8U4M2
    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
  FLPA_PYRFU | Q8U4M2
    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
        FLPA_PYRFU | Q8U4M2: 2nnw 3nmu 3nvk 3nvm 4by9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PRY)