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(-) Description

Title :  2.9 ANGSTROMS RESOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A VARIANT SURFACE GLYCOPROTEIN FROM TRYPANOSOMA BRUCEI
 
Authors :  D. Freymann, J. Down, D. C. Wiley
Date :  22 Oct 90  (Deposition) - 15 Jan 92  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Freymann, J. Down, M. Carrington, I. Roditi, M. Turner, D. Wiley
2. 9 A Resolution Structure Of The N-Terminal Domain Of A Variant Surface Glycoprotein From Trypanosoma Brucei.
J. Mol. Biol. V. 216 141 1990
PubMed-ID: 2231728  |  Reference-DOI: 10.1016/S0022-2836(05)80066-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VARIANT SURFACE GLYCOPROTEIN MITAT 1.2
    Chains: A, B
    Engineered: YES
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:38 , LYS A:41 , MET A:42 , TYR A:72 , ASN A:263 , GLU A:313 , NAG A:367BINDING SITE FOR RESIDUE NAG A 366
2AC2SOFTWAREALA A:45 , ARG A:48 , SER A:317 , GLY A:335 , NAG A:366 , BMA A:368BINDING SITE FOR RESIDUE NAG A 367
3AC3SOFTWAREGLY A:335 , NAG A:367BINDING SITE FOR RESIDUE BMA A 368
4AC4SOFTWARELYS B:38 , LYS B:41 , MET B:42 , TYR B:72 , ASN B:263 , GLU B:313 , NAG B:367BINDING SITE FOR RESIDUE NAG B 366
5AC5SOFTWAREALA B:45 , ARG B:48 , SER B:317 , GLY B:335 , NAG B:366 , MAN B:368BINDING SITE FOR RESIDUE NAG B 367
6AC6SOFTWAREGLY B:335 , NAG B:367BINDING SITE FOR RESIDUE MAN B 368

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:145
2A:123 -A:187
3B:15 -B:145
4B:123 -B:187

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VSG)

(-) Exons   (0, 0)

(no "Exon" information available for 1VSG)

(-) 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:362
 aligned with VSM2_TRYBB | P26332 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:362
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386  
           VSM2_TRYBB    27 AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQEVTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPIQPKRPAATYLGKAGYVGLTRQADAANNFHDNDAECRLASGHNTNGLGKSGQLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQPWIDAWKAKKALTGAETAEFRNETAGIAGKTGVTKLVEEALLKKKDSEASEIQTELKKYFSGHENEQWTAIEKLISEQPVAQNLVGDNQPTKLGELEGNAKLTTILAYYRMETAGKFEVLT 388
               SCOP domains d1vsga_ A: Variant surface glycoprotein (N-terminal domain)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1vsgA01 A:1-33,A:86-255          1vsgA02 A:34-85,A:256-362                           1vsgA01 A:1-33,A:86-255 Variant Surface Glycoprotein, subunit A domain 1                                                                                                  1vsgA02 A:34-85,A:256-362 Variant Surface Glycoprotein, subunit A, domain 2                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............................................................................................eeee....eeee.....eee..............hhhhhhhhhhhh.....................hhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vsg A   1 AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQEVTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPIQPKRPAATYLGKAGYVGLTRQADAANNFHDNDAECRLASGHNTNGLGKSGQLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQPWIDAWKAKKALTGAETAEFRNETAGIAGKTGVTKLVEEALLKKKDSEASEIQTELKKYFSGHENEQWTAIEKLISEQPVAQNLVGDNQPTKLGELEGNAKLTTILAYYRMETAGKFEVLT 362
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  


Chain B from PDB  Type:PROTEIN  Length:362
 aligned with VSM2_TRYBB | P26332 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:362
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386  
           VSM2_TRYBB    27 AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQEVTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPIQPKRPAATYLGKAGYVGLTRQADAANNFHDNDAECRLASGHNTNGLGKSGQLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQPWIDAWKAKKALTGAETAEFRNETAGIAGKTGVTKLVEEALLKKKDSEASEIQTELKKYFSGHENEQWTAIEKLISEQPVAQNLVGDNQPTKLGELEGNAKLTTILAYYRMETAGKFEVLT 388
               SCOP domains d1vsgb_ B: Variant surface glycoprotein (N-terminal domain)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1vsgB01 B:1-33,B:86-255          1vsgB02 B:34-85,B:256-362                           1vsgB01 B:1-33,B:86-255 Variant Surface Glycoprotein, subunit A domain 1                                                                                                  1vsgB02 B:34-85,B:256-362 Variant Surface Glycoprotein, subunit A, domain 2                                 CATH domains
           Pfam domains (1) Trypan_glycop-1vsgB01 B:1-355                                                                                                                                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) Trypan_glycop-1vsgB02 B:1-355                                                                                                                                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............................................................................................eeee....eeee.....eee..............hhhhhhhhhhhh.....................hhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vsg B   1 AAEKGFKQAFWQPLCQVSEELDDQPKGALFTLQAAASKIQKMRDAALRASIYAEINHGTNRAKAAVIVANHYAMKADSGLEALKQTLSSQEVTATATASYLKGRIDEYLNLLLQTKESGTSGCMMDTSGTNTVTKAGGTIGGVPCKLQLSPIQPKRPAATYLGKAGYVGLTRQADAANNFHDNDAECRLASGHNTNGLGKSGQLSAAVTMAAGYVTVANSQTAVTVQALDALQEASGAAHQPWIDAWKAKKALTGAETAEFRNETAGIAGKTGVTKLVEEALLKKKDSEASEIQTELKKYFSGHENEQWTAIEKLISEQPVAQNLVGDNQPTKLGELEGNAKLTTILAYYRMETAGKFEVLT 362
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Trypan_glycop] (1)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VSM2_TRYBB | P26332)
biological process
    GO:0020012    evasion or tolerance of host immune response    Any process, either active or passive, by which an organism avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
cellular component
    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: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

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        VSM2_TRYBB | P26332: 1xu6

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