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(-) Description

Title :  STRUCTURE OF DBL6 EPSILON DOMAIN FROM VAR2CSA
 
Authors :  P. Khunrae, M. K. Higgins
Date :  16 Feb 09  (Deposition) - 18 Aug 09  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane Protein, Chondroitin Sulphate A, Membrane Protein Dbl, Pfemp1, Malaria, Var2Csa (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Khunrae, J. M. D. Philip, D. R. Bull, M. K. Higgins
Structural Comparison Of Two Cspg-Binding Dbl Domains From The Var2Csa Protein Important In Malaria During Pregnancy.
J. Mol. Biol. V. 393 202 2009
PubMed-ID: 19695262  |  Reference-DOI: 10.1016/J.JMB.2009.08.027

(-) Compounds

Molecule 1 - ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1)
    Cell: ERYTHROCYTE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET15
    Expression System Vector Type: PLASMID
    Fragment: DBL6 EPSILON, RESIDUES 2333-2634
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Other Details: GENOMIC DNA FROM MR4
    Strain: 3D7
    Synonym: VAR2CSA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2WAU)

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:2520 -A:2604
2A:2534 -A:2551
3A:2539 -A:2633
4A:2555 -A:2631
5A:2598 -A:2602
6B:2520 -B:2604
7B:2534 -B:2551
8B:2555 -B:2631
9B:2598 -B:2602

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:2487 -Asn B:2488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WAU)

(-) Sequences/Alignments

Asymmetric 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:278
 aligned with Q8I639_PLAF7 | Q8I639 from UniProtKB/TrEMBL  Length:3056

    Alignment length:285
                                  2359      2369      2379      2389      2399      2409      2419      2429      2439      2449      2459      2469      2479      2489      2499      2509      2519      2529      2539      2549      2559      2569      2579      2589      2599      2609      2619      2629     
        Q8I639_PLAF7   2350 DTWTDLVKNSSDINKGVLLPPRRKNLFLKIDESDICKYKRDPKLFKDFIYSSAISEVERLKKVYGEAKTKVVHAMKYSFADIGSIIKGDDMMENNSSDKIGKILGDGVGQNEKRKKWWDMNKYHIWESMLCGYKHAYGNISENDRKMLDIPNNDDEHQFLRWFQEWTENFCTKRNELYENMVTACNSAKCNTSNGSVDKKECTEACKNYSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKCNGECSCLSEYFKDETRWKNPYETLDDTEVKNNCMCK 2634
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh.........-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......hhhhhhhh..hhhhh.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wau A 2350 DTWTDLVKNSSDINKGVLLPPRRKNLFLKIDESDICKYKRDPKLFKDFIYSSAISEVERLKKVYGEAKTKVVHAMKYSFADIGSIIKGDDMMENNSSDKIGKILGDGVGQNEKRKKWWDMNKYHIWESMLSGYKHAYGNISENDRKMLDIPNNDDEHQFLRWFQEWTENFCTKRNELYENMVTACNSAKC-------DKKECTEACKNYSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKCNGECSCLSEYFKDETRWKNPYETLDDTEVKNNCMCK 2634
                                  2359      2369      2379      2389      2399      2409      2419      2429      2439      2449      2459      2469      2479      2489      2499      2509      2519      2529      2539      2549      2559      2569      2579      2589      2599      2609      2619      2629     
                                                                                                                                                                                                                      2539    2547                                                                                       


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q8I639_PLAF7 | Q8I639 from UniProtKB/TrEMBL  Length:3056

    Alignment length:286
                                  2358      2368      2378      2388      2398      2408      2418      2428      2438      2448      2458      2468      2478      2488      2498      2508      2518      2528      2538      2548      2558      2568      2578      2588      2598      2608      2618      2628      
        Q8I639_PLAF7   2349 DDTWTDLVKNSSDINKGVLLPPRRKNLFLKIDESDICKYKRDPKLFKDFIYSSAISEVERLKKVYGEAKTKVVHAMKYSFADIGSIIKGDDMMENNSSDKIGKILGDGVGQNEKRKKWWDMNKYHIWESMLCGYKHAYGNISENDRKMLDIPNNDDEHQFLRWFQEWTENFCTKRNELYENMVTACNSAKCNTSNGSVDKKECTEACKNYSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKCNGECSCLSEYFKDETRWKNPYETLDDTEVKNNCMCK 2634
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Duffy_binding-2wauB01 B:2349-2600                                                                                                                                                                                                                           ---------------------------------- Pfam domains (1)
           Pfam domains (2) Duffy_binding-2wauB02 B:2349-2600                                                                                                                                                                                                                           ---------------------------------- Pfam domains (2)
         Sec.struct. author ....................hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh....hhhhhh..hhhhh........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wau B 2349 DDTWTDLVKNSSDINKGVLLPPRRKNLFLKIDESDICKYKRDPKLFKDFIYSSAISEVERLKKVYGEAKTKVVHAMKYSFADIGSIIKGDDMMENNSSDKIGKILGDGVGQNEKRKKWWDMNKYHIWESMLSGYKHAYGNISENDRKMLDIPNNDDEHQFLRWFQEWTENFCTKRNELYENMVTAC---------------ECTEACKNYSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKCNGECSCLSEYFKDETRWKNPYETLDDTEVKNNCMCK 2634
                                  2358      2368      2378      2388      2398      2408      2418      2428      2438      2448      2458      2468      2478      2488      2498      2508      2518      2528     |   -         - |    2558      2568      2578      2588      2598      2608      2618      2628      
                                                                                                                                                                                                                  2534            2550
   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 2WAU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DBL (4)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8I639_PLAF7 | Q8I639)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0020033    antigenic variation    Any process involved in the biological strategy of changing antigenic determinants on the surface that are exposed to another organism's immune system.
    GO:0020035    cytoadherence to microvasculature, mediated by symbiont protein    The adherence of symbiont-infected erythrocytes to microvascular endothelium via symbiont proteins embedded in the membrane of the erythrocyte.
    GO:0020013    modulation by symbiont of host erythrocyte aggregation    Any process in which a symbiont organism modulates the frequency, rate or extent of erythrocyte aggregation in its host organism, e.g. the binding of parasite-infected erythrocytes to uninfected erythrocytes.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0020030    infected host cell surface knob    Protrusion that develops in the plasma membrane of a parasitized erythrocyte. An example of this component is found in Plasmodium species.
    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.

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    Gly B:2487 - Asn B:2488   [ RasMol ]  
 
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