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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PLATELET ACTIVATOR CONVULXIN, A DISULFIDE LINKED A4B4 CYCLIC TETRAMER FROM THE VENOM OF CROTALUS DURISSUS TERRIFICUS
 
Authors :  M. T. Murakami, S. P. Zela, L. M. Gava, S. Michelan-Duarte, A. C. O. Cintra, R. K. Arni
Date :  28 Aug 03  (Deposition) - 21 Nov 03  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (4x)
Biol. Unit 2:  B,D  (4x)
Biol. Unit 3:  A (4x),B (4x),C (4x),D (4x)
Keywords :  Lectin, C-Type Lectin, Platelet, Sugar-Binding Protein, Activator, Snake Venom (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Murakami, S. P. Zela, L. M. Gava, S. Michelan-Duarte, A. C. O. Cintra, R. K. Arni
Crystal Structure Of The Platelet Activator Convulxin, A Disulfide Linked A4B4 Cyclic Tetramer From The Venom Of Crotalus Durissus Terrificus
Biochem. Biophys. Res. Commun. V. 310 478 2003
PubMed-ID: 14521935  |  Reference-DOI: 10.1016/J.BBRC.2003.09.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONVULXIN ALPHA
    Chains: A, B
    Organism Common: SOUTH AMERICAN RATTLESNAKE
    Organism Scientific: CROTALUS DURISSUS TERRIFICUS
    Organism Taxid: 8732
    Synonym: CVX ALPHA
    Tissue: VENOM GLAND
 
Molecule 2 - CONVULXIN BETA
    Chains: C, D
    Organism Common: SOUTH AMERICAN RATTLESNAKE
    Organism Scientific: CROTALUS DURISSUS TERRIFICUS
    Organism Taxid: 8732
    Synonym: CVX BETA
    Tissue: VENOM GLAND

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x): A C 
Biological Unit 2 (4x):  B D
Biological Unit 3 (4x): A (4x)B (4x)C (4x)D (4x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UMR)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:4 -A:15
2A:32 -A:129
3A:81 -C:277
4A:104 -A:121
5A:135 -C:203
6B:4 -B:15
7B:32 -B:129
8B:81 -D:277
9B:104 -B:121
10B:135 -D:203
11C:204 -C:215
12C:232 -C:321
13C:298 -C:313
14D:204 -D:215
15D:232 -D:321
16D:298 -D:313

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_CRODU34-153
 		  2A:11-130
B:11-130
SLB_CRODU34-145
 		  2C:211-322
D:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLB_CRODU121-144
 		  2C:298-321
D:298-321
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_CRODU34-153
 		  4A:11-130
-
SLB_CRODU34-145
 		  4C:211-322
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLB_CRODU121-144
 		  4C:298-321
-
Biological Unit 2 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_CRODU34-153
 		  4-
B:11-130
SLB_CRODU34-145
 		  4-
D:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLB_CRODU121-144
 		  4-
D:298-321
Biological Unit 3 (2, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_CRODU34-153
 		  8A:11-130
B:11-130
SLB_CRODU34-145
 		  8C:211-322
D:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLB_CRODU121-144
 		  8C:298-321
D:298-321

(-) Exons   (0, 0)

(no "Exon" information available for 1UMR)

(-) 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:135
 aligned with SLA_CRODU | O93426 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:135
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     
            SLA_CRODU    24 GLHCPSDWYYYDQHCYRIFNEEMNWEDAEWFCTKQAKGAHLVSIKSAKEADFVAWMVTQNIEESFSHVSIGLRVQNKEKQCSTKWSDGSSVSYDNLLDLYITKCSLLKKETGFRKWFVASCIGKIPFVCKFPPQC 158
               SCOP domains d1umra_ A: Snake coagglutinin alpha chain                                                                                               SCOP domains
               CATH domains 1umrA00 A:1-135 Mannose-Binding Protein A, subunit A                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.....eee..eee......................hhhhh..eeeee.hhh....eee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------C_TYPE_LECTIN_2  PDB: A:11-130 UniProt: 34-153                                                                          ----- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1umr A   1 GLHCPSDWYYYDQHCYRIFNEEMNWEDAEWFCTKQAKGAHLVSIKSAKEADFVAWMVTQNIEESFSHVSIGLRVQNKEKQCSTKWSDGSSVSYDNLLDLYITKCSLLKKETGFRKWFVASCIGKIPFVCKFPPQC 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with SLA_CRODU | O93426 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:135
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     
            SLA_CRODU    24 GLHCPSDWYYYDQHCYRIFNEEMNWEDAEWFCTKQAKGAHLVSIKSAKEADFVAWMVTQNIEESFSHVSIGLRVQNKEKQCSTKWSDGSSVSYDNLLDLYITKCSLLKKETGFRKWFVASCIGKIPFVCKFPPQC 158
               SCOP domains d1umrb_ B: Snake coagglutinin alpha chain                                                                                               SCOP domains
               CATH domains 1umrB00 B:1-135 Mannose-Binding Protein A, subunit A                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.....eee..eee......................hhhhh..eeeee.hhh....eee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------C_TYPE_LECTIN_2  PDB: B:11-130 UniProt: 34-153                                                                          ----- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1umr B   1 GLHCPSDWYYYDQHCYRIFNEEMNWEDAEWFCTKQAKGAHLVSIKSAKEADFVAWMVTQNIEESFSHVSIGLRVQNKEKQCSTKWSDGSSVSYDNLLDLYITKCSLLKKETGFRKWFVASCIGKIPFVCKFPPQC 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SLB_CRODU | O93427 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    33        43        53        63        73        83        93       103       113       123       133       143     
            SLB_CRODU    24 GFCCPSHWSSYDRYCYKVFKQEMTWADAEKFCTQQHTGSHLVSFHSTEEVDFVVKMTHQSLKSTFFWIGANNIWNKCNWQWSDGTKPEYKEWHEEFECLISRTFDNQWLSAPCSDTYSFVCKFEA 148
               SCOP domains d1umrc_ C: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1umrC00 C:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh.....eee...........eee...............eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: C:211-322 UniProt: 34-145                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1umr C 201 GFCCPSHWSSYDRYCYKVFKQEMTWADAEKFCTQQHTGSHLVSFHSTEEVDFVVKMTHQSLKSTFFWIGANNIWNKCNWQWSDGTKPEYKEWHEEFECLISRTFDNQWLSAPCSDTYSFVCKFEA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320     


Chain D from PDB  Type:PROTEIN  Length:125
 aligned with SLB_CRODU | O93427 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    33        43        53        63        73        83        93       103       113       123       133       143     
            SLB_CRODU    24 GFCCPSHWSSYDRYCYKVFKQEMTWADAEKFCTQQHTGSHLVSFHSTEEVDFVVKMTHQSLKSTFFWIGANNIWNKCNWQWSDGTKPEYKEWHEEFECLISRTFDNQWLSAPCSDTYSFVCKFEA 148
               SCOP domains d1umrd_ D: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1umrD00 D:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeeehhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh...eee...........eee...............eeeeee.....eeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: D:211-322 UniProt: 34-145                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1umr D 201 GFCCPSHWSSYDRYCYKVFKQEMTWADAEKFCTQQHTGSHLVSFHSTEEVDFVVKMTHQSLKSTFFWIGANNIWNKCNWQWSDGTKPEYKEWHEEFECLISRTFDNQWLSAPCSDTYSFVCKFEA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UMR)

(-) Gene Ontology  (1, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SLA_CRODU | O93426)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain C,D   (SLB_CRODU | O93427)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  SLA_CRODU | O93426
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  SLB_CRODU | O93427
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 Related Entries

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

UniProtKB/Swiss-Prot
        SLA_CRODU | O93426: 1uos
        SLB_CRODU | O93427: 1uos

(-) Related Entries Specified in the PDB File

1c3a STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS