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(-) Description

Title :  THE MOUSE VON WILLEBRAND FACTOR A1-BOTROCETIN COMPLEX
 
Authors :  K. Fukuda, R. C. Liddington
Date :  14 Jul 04  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rossmann Fold, C-Type Lectin Fold, Protein-Protein Complex, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Fukuda, T. Doggett, I. J. Laurenzi, R. C. Liddington, T. G. Diacovo
The Snake Venom Protein Botrocetin Acts As A Biological Brace To Promote Dysfunctional Platelet Aggregation
Nat. Struct. Mol. Biol. V. 12 152 2005
PubMed-ID: 15665869  |  Reference-DOI: 10.1038/NSMB892
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BOTROCETIN
    ChainsA
    FragmentALPHA CHAIN
    Organism CommonJARARACA
    Organism ScientificBOTHROPS JARARACA
    Organism Taxid8724
    SecretionVENOM
    SynonymPLATELET COAGGLUTININ
 
Molecule 2 - BOTROCETIN
    ChainsB
    FragmentBETA CHAIN
    Organism CommonJARARACA
    Organism ScientificBOTHROPS JARARACA
    Organism Taxid8724
    SecretionVENOM
    SynonymPLATELET COAGGLUTININ
 
Molecule 3 - VON WILLEBRAND FACTOR
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentVWF A1
    GeneVWF
    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 1U0O)

(-) Sites  (0, 0)

(no "Site" information available for 1U0O)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:13
2A:30 -A:128
3A:80 -B:275
4A:103 -A:120
5B:202 -B:213
6B:230 -B:321
7B:298 -B:313
8C:509 -C:695

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U0O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0O)

(-) PROSITE Motifs  (3, 4)

Asymmetric/Biological Unit (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLEA_BOTJA9-129  1A:9-129
SLEB_BOTJA9-122  1B:209-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLEA_BOTJA103-128  1A:103-128
3VWFAPS50234 VWFA domain profile.VWF_MOUSE1498-1665
1277-1453
1691-1871
  1-
C:514-690
-

(-) Exons   (0, 0)

(no "Exon" information available for 1U0O)

(-) 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:133
 aligned with SLEA_BOTJA | P22029 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
          SLEA_BOTJA      1 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP  133
               SCOP domains d1u0oa_ A: Snake coagglutinin alpha chain                                                                                             SCOP domains
               CATH domains 1u0oA00 A:1-133 Mannose-Binding Protein A, subunit A                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeeeeeeehhhhhhhhhh......ee......hhhhhhhhhhhhhhh.....eeeeeeee.............................eeeeehhhhhheeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:9-129 UniProt: 9-129                                                                             ---- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ----- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u0o A    1 DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP  133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SLEB_BOTJA | P22030 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
          SLEB_BOTJA      1 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA  125
               SCOP domains d1u0ob_ B: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1u0oB00 B:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhh........ee...........eee......hhhhhh.....eeeeee....eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: B:209-322 UniProt: 9-122                                                                    --- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                1u0o B  201 DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA  325
                                   210       220       230       240       250       260       270       280       290       300       310       320     

Chain C from PDB  Type:PROTEIN  Length:196
 aligned with VWF_MOUSE | Q8CIZ8 from UniProtKB/Swiss-Prot  Length:2813

    Alignment length:196
                                  1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      
           VWF_MOUSE   1270 FYCSKLLDLVFLLDGSSMLSEAEFEVLKAFVVGMMERLHISQKRIRVAVVEYHDGSRAYLELKARKRPSELRRITSQIKYTGSQVASTSEVLKYTLFQIFGKIDRPEASHITLLLTASQEPPRMARNLVRYVQGLKKKKVIVIPVGIGPHASLKQIRLIEKQAPENKAFLLSGVDELEQRRDEIVSYLCDLAPEAP 1465
               SCOP domains d1u0oc1 C:507-702 von Willebrand factor A1 domain, vWA1                                                                                                                                              SCOP domains
               CATH domains 1u0oC00 C:507-702  [code=3.40.50.410, no name defined]                                                                                                                                               CATH domains
               Pfam domains -------VWA-1u0oC01 C:514-691                                                                                                                                                             ----------- Pfam domains
         Sec.struct. author ......eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeeeee...eeeee......hhhhhhhhhhh.........hhhhhhhhhhhh..........eeeeeeee....hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------VWFA  PDB: C:514-690 UniProt: 1277-1453                                                                                                                                          ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u0o C  507 FYCSKLLDLVFLLDGSSMLSEAEFEVLKAFVVGMMERLHISQKRIRVAVVEYHDGSRAYLELKARKRPSELRRITSQIKYTGSQVASTSEVLKYTLFQIFGKIDRPEASHITLLLTASQEPPRMARNLVRYVQGLKKKKVIVIPVGIGPHASLKQIRLIEKQAPENKAFLLSGVDELEQRRDEIVSYLCDLAPEAP  702
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696      

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)

(-) Gene Ontology  (24, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLEA_BOTJA | P22029)
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 B   (SLEB_BOTJA | P22030)
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   (VWF_MOUSE | Q8CIZ8)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019865    immunoglobulin binding    Interacting selectively and non-covalently with an immunoglobulin.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0031589    cell-substrate adhesion    The attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    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.
cellular component
    GO:0033093    Weibel-Palade body    A large, elongated, rod-shaped secretory granule characteristic of vascular endothelial cells that contain a number of structurally and functionally distinct proteins, of which the best characterized are von Willebrand factor (VWF) and P-selectin. Weibel-Palade bodies are formed from the trans-Golgi network in a process that depends on VWF, which is densely packed in a highly organized manner, and on coat proteins that remain associated with the granules. Upon cell stimulation, regulated exocytosis releases the contained proteins to the cell surface, where they act in the recruitment of platelets and leukocytes and in inflammatory and vasoactive responses.
    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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SLEA_BOTJA | P220291fvu 1ijk 1u0n
        SLEB_BOTJA | P220301fvu 1ijk 1u0n

(-) Related Entries Specified in the PDB File

1auq THE HUMAN A1 WILD TYPE
1ijb THE MUTANT (I546V) A1
1ijk THE MUTANT (I546V):BOTROCETIN COMPLEX
1u0n