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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: COMPLEX WITH PHENYLMERCURY
 
Authors :  S. Macedo-Ribeiro, W. Bode, R. Huber, W. H. Kane, P. Fuentes-Prior
Date :  07 Sep 99  (Deposition) - 26 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Coagulation, Membrane-Binding, Discoidin Family, Calcium- Independent, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Macedo-Ribeiro, W. Bode, R. Huber, M. A. Quinn-Allen, S. W. Kim, T. L. Ortel, G. P. Bourenkov, H. D. Bartunik, M. T. Stubbs, W. H. Kane, P. Fuentes-Prior
Crystal Structures Of The Membrane-Binding C2 Domain Of Human Coagulation Factor V.
Nature V. 402 434 1999
PubMed-ID: 10586886  |  Reference-DOI: 10.1038/46594
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (COAGULATION FACTOR V)
    ChainsA
    EngineeredYES
    Expression System CommonBACULOVIRUS-DRIVEN INSECT CELL SYSTEM
    FragmentC2 DISCOIDIN-LIKE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymACTIVATED PROTEIN C COFACTOR
    TissueBLOOD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PHG1Ligand/IonPHENYLMERCURY

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:48 , CYS A:76 , MET A:83 , HOH A:216BINDING SITE FOR RESIDUE PHG A 296

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1 -A:156

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:128 -Pro A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032701R2102CFA5_HUMANDisease (FA5D)118203910AR37C
2UniProtVAR_017329R2102HFA5_HUMANDisease (THPH2)  ---AR37H
3UniProtVAR_021302M2148TFA5_HUMANPolymorphism9332701AM83T
4UniProtVAR_034603K2185RFA5_HUMANPolymorphism6679078AK120R
5UniProtVAR_013899D2222GFA5_HUMANPolymorphism6027AD157G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.FA5_HUMAN1907-2061
2066-2221
  1-
A:1-156
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.FA5_HUMAN1947-1980
2111-2140
  1-
A:46-75
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.FA5_HUMAN2045-2061
2205-2221
  1-
A:140-156

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003677971ENSE00001673787chr1:169555826-169555467360FA5_HUMAN1-53530--
1.2ENST000003677972ENSE00000789613chr1:169551760-16955166992FA5_HUMAN53-84320--
1.3ENST000003677973ENSE00000789612chr1:169541581-169541459123FA5_HUMAN84-125420--
1.4ENST000003677974ENSE00000789611chr1:169530004-169529792213FA5_HUMAN125-196720--
1.5ENST000003677975ENSE00000789610chr1:169528534-169528391144FA5_HUMAN196-244490--
1.6ENST000003677976ENSE00001435704chr1:169526105-169525884222FA5_HUMAN244-318750--
1.7ENST000003677977ENSE00001435673chr1:169524585-169524420166FA5_HUMAN318-373560--
1.8ENST000003677978ENSE00000789607chr1:169521972-169521795178FA5_HUMAN373-432600--
1.9ENST000003677979ENSE00000789606chr1:169519977-169519878100FA5_HUMAN433-466340--
1.10ENST0000036779710ENSE00000789605chr1:169519253-169519039215FA5_HUMAN466-537720--
1.11ENST0000036779711ENSE00000789604chr1:169515830-169515680151FA5_HUMAN538-588510--
1.12bENST0000036779712bENSE00000789603chr1:169513746-169513534213FA5_HUMAN588-659720--
1.13ENST0000036779713ENSE00000814494chr1:169512352-1695095322821FA5_HUMAN659-15999410--
1.14ENST0000036779714ENSE00000814495chr1:169505918-169505744175FA5_HUMAN1599-1657590--
1.15ENST0000036779715ENSE00000814496chr1:169500260-169500024237FA5_HUMAN1658-1736790--
1.16ENST0000036779716ENSE00001376235chr1:169499056-169498846211FA5_HUMAN1737-1807710--
1.17ENST0000036779717ENSE00001388919chr1:169497332-169497153180FA5_HUMAN1807-1867610--
1.18ENST0000036779718ENSE00001367181chr1:169495255-169495139117FA5_HUMAN1867-1906400--
1.19ENST0000036779719ENSE00001168291chr1:169494146-16949407572FA5_HUMAN1906-1930250--
1.20ENST0000036779720ENSE00001168281chr1:169493142-169493039104FA5_HUMAN1930-1964350--
1.21ENST0000036779721ENSE00000814502chr1:169492590-169492435156FA5_HUMAN1965-2016520--
1.22ENST0000036779722ENSE00000814503chr1:169489902-169489758145FA5_HUMAN2017-2065491A:0-01
1.23ENST0000036779723ENSE00001168273chr1:169487801-169487650152FA5_HUMAN2065-2115511A:0-5051
1.24bENST0000036779724bENSE00000814505chr1:169484864-169484682183FA5_HUMAN2116-2176611A:51-11161
1.25ENST0000036779725ENSE00001627321chr1:169483697-169483404294FA5_HUMAN2177-2224481A:112-15948

(-) 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:160
 aligned with FA5_HUMAN | P12259 from UniProtKB/Swiss-Prot  Length:2224

    Alignment length:160
                                  2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224
           FA5_HUMAN   2065 GCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY 2224
               SCOP domains d1czsa_ A: C2 domain of factor V                                                                                                                                 SCOP domains
               CATH domains 1czsA00 A:0-159 Galactose-binding domain-like                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhheeeee...........hhhhh....................eeeee........eeeeee.........eeeeeeeee...................eeeee.....eeeee.......eeeee..........eeeee..... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------C---------------------------------------------T------------------------------------R------------------------------------G-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------H-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -FA58C_3  PDB: A:1-156 UniProt: 2066-2221                                                                                                                    --- PROSITE (1)
                PROSITE (2) ----------------------------------------------FA58C_1  PDB: A:46-75         ----------------------------------------------------------------FA58C_2          --- PROSITE (2)
           Transcript 1 (1) 1--------------------------------------------------Exon 1.24b  PDB: A:51-111 UniProt: 2116-2176                 Exon 1.25  PDB: A:112-159 UniProt: 2177-2224     Transcript 1 (1)
           Transcript 1 (2) Exon 1.23  PDB: A:0-50 UniProt: 2065-2115          ------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1czs A    0 GCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSITLRLELFGCDIY  159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FA5_HUMAN | P12259)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    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.
    GO:0031091    platelet alpha granule    A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA5_HUMAN | P122591czt 1czv 1fv4 1y61 3p6z 3p70 3s9c

(-) Related Entries Specified in the PDB File

1czt 1czv