Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEIN RPRP(90-231) , 25 STRUCTURES
 
Authors :  T. L. James, H. Liu, N. B. Ulyanov, S. Farr-Jones
Date :  25 Nov 98  (Deposition) - 02 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Prion, Scrapie, Brain, Glycoprotein, Prion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. L. James, H. Liu, N. B. Ulyanov, S. Farr-Jones, H. Zhang, D. G. Donne, K. Kaneko, D. Groth, I. Mehlhorn, S. B. Prusiner, F. E. Cohen
Solution Structure Of A 142-Residue Recombinant Prion Protein Corresponding To The Infectious Fragment Of The Scrapie Isoform.
Proc. Natl. Acad. Sci. Usa V. 94 10086 1997
PubMed-ID: 9294167  |  Reference-DOI: 10.1073/PNAS.94.19.10086
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PRION PROTEIN)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Atcc Number55244
    Expression System Cellular LocationPERIPLASM
    Expression System GeneALKALINE PHOSPHATASE
    Expression System PlasmidSTII VARIANT 4 (90 - 231)
    Expression System Strain27C7
    Expression System Taxid562
    Expression System VectorESCHERICHIA COLI 27C7
    Expression System Vector TypePLASMID SECRETION VESICLE 9
    Fragment90 - 231
    Organism CommonGOLDEN HAMSTER
    Organism ScientificMESOCRICETUS AURATUS
    Organism Taxid10036
    Other DetailsGENENTECH DERIVED VECTOR SYSTEM
    SynonymSHA RPRP90-231

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1B10)

(-) Sites  (0, 0)

(no "Site" information available for 1B10)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:179 -A:214

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B10)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B10)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRION_2PS00706 Prion protein signature 2.PRIO_MESAU200-218  1A:200-218

(-) Exons   (0, 0)

(no "Exon" information available for 1B10)

(-) Sequences/Alignments

NMR Structure
   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:104
 aligned with PRIO_MESAU | P04273 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:104
                                   134       144       154       164       174       184       194       204       214       224    
           PRIO_MESAU   125 LGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDG 228
               SCOP domains d1b10a_ A: Prion protein domain                                                                          SCOP domains
               CATH domains 1b10A00 A:125-228 Major Prion Protein                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee............hhhhhhhhhh.......eee........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------PRION_2            ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1b10 A 125 LGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDG 228
                                   134       144       154       164       174       184       194       204       214       224    

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B10)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (PRIO_MESAU | P04273)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

NMR Structure
  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 1b10)
 
  Sites
(no "Sites" information available for 1b10)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1b10)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1b10
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRIO_MESAU | P04273
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PRIO_MESAU | P04273
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_MESAU | P042732kkg 2lh8 3nve 4yxl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B10)