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(-) Description

Title :  STRUCTURE OF AN ANTI-PRP FAB, P-CLONE, IN COMPLEX WITH ITS COGNATE BOVINE PEPTIDE EPITOPE.
 
Authors :  Z. K. Kanyo
Date :  27 Jun 06  (Deposition) - 26 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Prion, Prp, Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Luginbuhl, Z. Kanyo, R. M. Jones, R. J. Fletterick, S. B. Prusiner, F. E. Cohen, R. A. Williamson, D. R. Burton, A. Pluckthun
Directed Evolution Of An Anti-Prion Protein Scfv Fragment To An Affinity Of 1 Pm And Its Structural Interpretation
J. Mol. Biol. V. 363 75 2006
PubMed-ID: 16962610  |  Reference-DOI: 10.1016/J.JMB.2006.07.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGHT CHAIN, P-CLONE FAB, CHIMERA
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Fragment2-109 (MOUSE), 110-271 (HUMAN)
    Organism CommonHOUSE MOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090,9606
    Strain,
 
Molecule 2 - HEAVY CHAIN, P-CLONE FAB, CHIMERA
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHOUSE MOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090,9606
    Strain,
 
Molecule 3 - PRION PROTEIN
    ChainsP
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN BOVINES.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2HH0)

(-) Sites  (0, 0)

(no "Site" information available for 2HH0)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:106
2H:181 -H:252
3L:23 -L:106
4L:181 -L:252

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Phe L:135 -Pro L:136
3Tyr L:187 -Pro L:188
4Phe H:187 -Pro H:188
5Glu H:191 -Pro H:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HH0)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000402921ENSBTAE00000340808chr13:47214467-4721451953PRIO_BOVIN-00--
1.2ENSBTAT000000402922ENSBTAE00000340806chr13:47216955-4721705298PRIO_BOVIN-00--
1.3ENSBTAT000000402923ENSBTAE00000310243chr13:47230279-472343694091PRIO_BOVIN1-2682681P:2-109

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d2hh0h1 H:1-149 Immunoglobulin heavy chain variable domain, VH                                                        d2hh0h2 H:152-271 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   - SCOP domains
               CATH domains 2hh0H01 H:1-149 Immunoglobulins                                                                                       2hh0H02 H:152-271 Immunoglobulins                                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.hhhhh.....eeeee........eeeee........eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hh0 H   1 VQLLEQSGAELVKPGASVKLSCTASGFNIEDSYIHWVKQRPEQGLEWIGRIDPEDGETKYAPKFQGKATITADTSSNTAYLHLRRLTSEDTAIYYCGRGAYYIKEDFWGQGTTLTVSSASTKGPSVFPLAPSSKAGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPA 272
                                  ||11        21     || 32||      47        57   ||   70        80        90       100       110 ||    141       153       163     ||178       188|      200 ||    214     ||230       240 ||    253    || 265       
                                  7|                27|  33|                    61|                                            112|            149|              169|          188|        202|          220|            242|         258|           
                                   9                 29   39                     65                                             134             152               175           191         207           227             246          261           

Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d2hh0l1 L:2-149 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d2hh0l2 L:153-271 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 2hh0L01 L:2-149 Immunoglobulins                                                                            2hh0L02 L:153-271 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eeee.....eeeeee........eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hh0 L   2 LVMTQTPSSLSASLGERVSLTCRASQDIGNNLNWIQQKPDGTIKRLIYATSSLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQHDTFPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 271
                                    11        21    ||  39        49        67        77      ||89        99       109 ||    142      |155       165    || 178       188|      200  ||   212       227       237    || 249       261       271
                                                   26| 32|                 58|               84|                     111|           149|              170|           188|         203|            221|            242|          258|          
                                                    29  39                  67                87                      135            153               174            191          206             227             245           261          

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with PRIO_BOVIN | P10279 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:9
           PRIO_BOVIN   107 HGQWNKPSK 115
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.3  Transcript 1
                 2hh0 P   2 HGQWNKPSK  10

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HH0)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (PRIO_BOVIN | P10279)
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 H:191 - Pro H:192   [ RasMol ]  
    Phe H:187 - Pro H:188   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_BOVIN | P102791dwy 1dwz 1dx0 1dx1 1skh 2rsk 2ru7 4yx2

(-) Related Entries Specified in the PDB File

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