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(-) Description

Title :  SOLUTION NMR STRUCTURE OF H2H3 DOMAIN OF OVINE PRION PROTEIN (RESIDUES 167-234)
 
Authors :  A. Pastore, M. Adrover, K. Pauwels, C. De Chiara, S. Prigent, H. Rezeai
Date :  04 Feb 10  (Deposition) - 07 Apr 10  (Release) - 18 Mar 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (12x)
NMR Structure *:  A  (1x)
Keywords :  H2H3, Prion Protein, Peptide Folding, Fibrilization Core, Cell Membrane, Membrane, Prion, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Adrover, K. Pauwels, S. Prigent, C. De Chiara, Z. Xu, C. Chapuis, A. Pastore, H. Rezaei
Prion Fibrillization Is Mediated By A Native Structural Element That Comprises Helices H2 And H3.
J. Biol. Chem. V. 285 21004 2010
PubMed-ID: 20375014  |  Reference-DOI: 10.1074/JBC.M110.111815

(-) Compounds

Molecule 1 - MAJOR PRION PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPET-28A
    Expression System Vector TypeVECTOR
    FragmentH2H3 FRAGMENT
    GenePRNP
    MutationYES
    Organism CommonDOMESTIC SHEEP,LAMBS,WILD SHEEP
    Organism ScientificOVIS ARIES
    Organism Taxid9940
    StrainSUFFOLK
    VariantARQ

 Structural Features

(-) Chains, Units

  1
NMR Structure (12x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KTM)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:182 -A:217

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PRIO_SHEEP_006 *R171HPRIO_SHEEP  ---  ---AQ171H
2UniProtVAR_PRIO_SHEEP_007 *R171QPRIO_SHEEP  ---  ---AQ171Q
3UniProtVAR_PRIO_SHEEP_008 *R211QPRIO_SHEEP  ---  ---AR211Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PRIO_SHEEP_006 *R171HPRIO_SHEEP  ---  ---AQ171H
2UniProtVAR_PRIO_SHEEP_007 *R171QPRIO_SHEEP  ---  ---AQ171Q
3UniProtVAR_PRIO_SHEEP_008 *R211QPRIO_SHEEP  ---  ---AR211Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRION_2PS00706 Prion protein signature 2.PRIO_SHEEP203-221  1A:203-221
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRION_2PS00706 Prion protein signature 2.PRIO_SHEEP203-221  1A:203-221

(-) Exons   (0, 0)

(no "Exon" information available for 2KTM)

(-) 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:68
 aligned with PRIO_SHEEP | P23907 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:68
                                   176       186       196       206       216       226        
           PRIO_SHEEP   167 RPVDRYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS 234
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains Prion-2ktmA01 A:167-234                                              Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
             SAPs(SNPs) (1) ----H---------------------------------------Q----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----Q--------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------PRION_2            ------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2ktm A 167 RPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKAMERVVEQMCITQYQRESQAYYQRGAS 234
                                   176       186       196       206       216       226        

Chain A from PDB  Type:PROTEIN  Length:68
 aligned with Q072G4_SHEEP | Q072G4 from UniProtKB/TrEMBL  Length:256

    Alignment length:68
                                   176       186       196       206       216       226        
         Q072G4_SHEEP   167 RPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS 234
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains Prion-2ktmA01 A:167-234                                              Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
             SAPs(SNPs) (1) ----H---------------------------------------Q----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----Q--------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2ktm A 167 RPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKAMERVVEQMCITQYQRESQAYYQRGAS 234
                                   176       186       196       206       216       226        

   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 2KTM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (30, 34)

NMR Structure(hide GO term definitions)
Chain A   (PRIO_SHEEP | P23907)
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.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015631    tubulin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules.
biological process
    GO:0071280    cellular response to copper ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0046007    negative regulation of activated T cell proliferation    Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0070885    negative regulation of calcineurin-NFAT signaling cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032700    negative regulation of interleukin-17 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
    GO:0032703    negative regulation of interleukin-2 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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.
    GO:1901379    regulation of potassium ion transmembrane transport    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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.

Chain A   (Q072G4_SHEEP | Q072G4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_SHEEP | P239071g04 1m25 1s4t 1tpx 1tqb 1tqc 1uw3 1xyu 1y2s 2mv8 2mv9 2n53 2rmv 2rmw

(-) Related Entries Specified in the PDB File

1tpx 1tqb 1xyu 1y2s