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(-) Description

Title :  OVINE RECOMBINANT PRP(114-234), VRQ VARIANT IN COMPLEX WITH THE FAB OF THE VRQ14 ANTIBODY
 
Authors :  F. Eghiaian, J. Grosclaude, P. Debey, B. Doublet, E. Treguer, H. Rezaei, M. Knossow
Date :  17 Jun 04  (Deposition) - 06 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Prion, Antibody, Unknown Function/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Eghiaian, J. Grosclaude, S. Lesceu, P. Debey, B. Doublet, E. Treguer, H. Rezaei, M. Knossow
Insight Into The Prpc-->Prpsc Conversion From The Structures Of Antibody-Bound Ovine Prion Scrapie-Susceptibility Variants
Proc. Natl. Acad. Sci. Usa V. 101 10254 2004
PubMed-ID: 15240887  |  Reference-DOI: 10.1073/PNAS.0400014101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRION PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-A
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentVRQ VARIANT, RESIDUES 127-228
    GenePRNP SHEEP VRQ VARIANT
    Organism CommonSHEEP
    Organism ScientificOVIS ARIES
    Organism Taxid9940
    SynonymOVPRP
 
Molecule 2 - VRQ14 FAB HEAVY CHAIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentVRQ14 FAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - VRQ14 FAB LIGHT CHAIN
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentVRQ14 FAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1TQB)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:182 -A:217
2B:140 -B:206
3C:23 -C:88
4C:134 -C:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe B:146 -Pro B:147
2Glu B:148 -Pro B:149
3Trp B:197 -Pro B:198
4Thr C:7 -Pro C:8
5Phe C:94 -Pro C:95
6Tyr C:140 -Pro C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric/Biological Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PRIO_SHEEP_002 *A136VPRIO_SHEEP  ---  ---AV136V
2UniProtVAR_PRIO_SHEEP_003 *M137TPRIO_SHEEP  ---  ---AM137T
3UniProtVAR_PRIO_SHEEP_004 *L141FPRIO_SHEEP  ---  ---AL141F
4UniProtVAR_PRIO_SHEEP_005 *R154HPRIO_SHEEP  ---  ---AR154H
5UniProtVAR_PRIO_SHEEP_006 *R171HPRIO_SHEEP  ---  ---AQ171H
6UniProtVAR_PRIO_SHEEP_007 *R171QPRIO_SHEEP  ---  ---AQ171Q
7UniProtVAR_PRIO_SHEEP_008 *R211QPRIO_SHEEP  ---  ---AR211Q
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (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 1TQB)

(-) 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:102
 aligned with PRIO_SHEEP | P23907 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:102
                                   136       146       156       166       176       186       196       206       216       226  
           PRIO_SHEEP   127 GLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDRYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAY 228
               SCOP domains d1tqba_ A: Prion protein domain                                                                        SCOP domains
               CATH domains 1tqbA00 A:127-228 Major Prion Protein                                                                  CATH domains
               Pfam domains ----------Prion-1tqbA01 A:137-228                                                                      Pfam domains
         Sec.struct. author .....ee.............hhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ---------VT---F------------H----------------H---------------------------------------Q----------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------Q--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------PRION_2            ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1tqb A 127 GLGGYMLGSVMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQRESQAY 228
                                   136       146       156       166       176       186       196       206       216       226  

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1tqbb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                   d1tqbb2 B:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1tqbB01 B:1-113 Immunoglobulins                                                                                  1tqbB02 B:114-223 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee...ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tqb B   1 QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNLVKQAPGKGFEWMGWINTFTGEPTYADDFKGRFVFSLDTSASTAYLQINNLKNEDTATYFFTRGTDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP 223
                                    10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       130       140       150 ||||  165 ||    176 ||    188     ||200   ||  211       221  
                                                                              52A                            82A||            96|                                                152|||    167|      178|          194| || 204|                 
                                                                                                              82B|            101                                                 154||     169       181           196 ||  206                 
                                                                                                               82C                                                                 155|                               198|                      
                                                                                                                                                                                    160                                200                      

Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1tqbc1 C:1-107 Immunoglobulin heavy chain variable domain, VH                                                  d1tqbc2 C:108-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                             SCOP domains
               CATH domains 1tqbC01 C:1-108 Immunoglobulins                                                                                  1tqbC02 C:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tqb C   1 DVVMSQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSRLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGIYFCWQGSHFPQTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20       29A| |||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                       29A| |||                                                                                                                                                                                        
                                                        29B |||                                                                                                                                                                                        
                                                          30A||                                                                                                                                                                                        
                                                           30B|                                                                                                                                                                                        
                                                            30C                                                                                                                                                                                        

   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  (3, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(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.

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    Glu B:148 - Pro B:149   [ RasMol ]  
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1tqc OVINE RECOMBINANT PRP(114-234), ARR VARIANT IN COMPLEX WITH THE VRQ14 FAB FRAGMENT (IGG2A)