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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CENTRAL REGION OF BOVINE FIBRINOGEN (E5 FRAGMENT) AT 1.4 ANGSTROMS RESOLUTION
 
Authors :  J. Madrazo, J. H. Brown, S. Litvinovich, R. Dominguez, S. Yakovlev, L. Medved, C. Cohen
Date :  10 Sep 01  (Deposition) - 17 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  N,O,P,Q,R,S
Keywords :  Fibrinogen, Fragment E, Disulfide Bonds, Asymmetry, Coiled- Coil, Beta-Sheet, Crystal Structure, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Madrazo, J. H. Brown, S. Litvinovich, R. Dominguez, S. Yakovlev, L. Medved, C. Cohen
Crystal Structure Of The Central Region Of Bovine Fibrinogen (E5 Fragment) At 1. 4-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 98 11967 2001
PubMed-ID: 11593005  |  Reference-DOI: 10.1073/PNAS.211439798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRINOGEN ALPHA CHAIN
    Chains: N, Q
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: PROTEOLYTIC FRAGMENT
 
Molecule 2 - FIBRINOGEN BETA CHAIN
    Chains: O, R
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: PROTEOLYTIC FRAGMENT
 
Molecule 3 - FIBRINOGEN GAMMA-B CHAIN
    Chains: P, S
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: PROTEOLYTIC FRAGMENT

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : NOPQRS

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1JY2)

(-) Sites  (0, 0)

(no "Site" information available for 1JY2)

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1N:39 -R:72
2N:48 -P:23
3N:52 -O:83
4O:72 -Q:39
5O:87 -P:19
6P:8 -S:9
7P:9 -S:8
8Q:48 -S:23
9Q:52 -R:83
10R:87 -S:19

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JY2)

(-) Exons   (0, 0)

(no "Exon" information available for 1JY2)

(-) 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 N from PDB  Type:PROTEIN  Length:43
 aligned with FIBA_BOVIN | P02672 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:43
                                    63        73        83        93   
           FIBA_BOVIN    54 GWPFCSDEDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLF  96
               SCOP domains d1jy2n_ N: Fibrinogen alpha chain           SCOP domains
               CATH domains 1jy2N00 N:35-77                             CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 1jy2 N  35 GWPFCSDEDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLF  77
                                    44        54        64        74   


Chain O from PDB  Type:PROTEIN  Length:51
 aligned with FIBB_BOVIN | P02676 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:51
                                    73        83        93       103       113 
           FIBB_BOVIN    64 RKPPDADGCLHADPDLGVLCPTGCKLQDTLVRQERPIRKSIEDLRNTVDSV 114
               SCOP domains d1jy2o_ O: Fibrinogen beta chain                    SCOP domains
               CATH domains 1jy2O00 O:64-114  [code=1.20.5.50, no name defined] CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 1jy2 O  64 RKPPDADGCLHADPDLGVLCPTGCKLQDTLVRQERPIRKSIEDLRNTVDSV 114
                                    73        83        93       103       113 


Chain P from PDB  Type:PROTEIN  Length:44
 aligned with FIBG_BOVIN | P12799 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:44
                                    38        48        58        68    
           FIBG_BOVIN    29 RDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLRTLEGILY  72
               SCOP domains d1jy2p_ P: Fibrinogen gamma chain            SCOP domains
               CATH domains 1jy2P00 P:5-48                               CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .............eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 1jy2 P   5 RDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLRTLEGILY  48
                                    14        24        34        44    


Chain Q from PDB  Type:PROTEIN  Length:43
 aligned with FIBA_BOVIN | P02672 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:43
                                    63        73        83        93   
           FIBA_BOVIN    54 GWPFCSDEDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLF  96
               SCOP domains d1jy2q_ Q: Fibrinogen alpha chain           SCOP domains
               CATH domains 1jy2Q00 Q:35-77                             CATH domains
           Pfam domains (1) Fib_alpha-1jy2Q01 Q:35-77                   Pfam domains (1)
           Pfam domains (2) Fib_alpha-1jy2Q02 Q:35-77                   Pfam domains (2)
         Sec.struct. author .....hhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 1jy2 Q  35 GWPFCSDEDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLF  77
                                    44        54        64        74   


Chain R from PDB  Type:PROTEIN  Length:50
 aligned with FIBB_BOVIN | P02676 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:50
                                    73        83        93       103       113
           FIBB_BOVIN    64 RKPPDADGCLHADPDLGVLCPTGCKLQDTLVRQERPIRKSIEDLRNTVDS 113
               SCOP domains d1jy2r_ R: Fibrinogen beta chain                   SCOP domains
               CATH domains 1jy2R00 R:64-113                                   CATH domains
           Pfam domains (1) ---Fib_alpha-1jy2R01 R:67-113                      Pfam domains (1)
           Pfam domains (2) ---Fib_alpha-1jy2R02 R:67-113                      Pfam domains (2)
         Sec.struct. author ........ee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 1jy2 R  64 RKPPDADGCLHADPDLGVLCPTGCKLQDTLVRQERPIRKSIEDLRNTVDS 113
                                    73        83        93       103       113


Chain S from PDB  Type:PROTEIN  Length:47
 aligned with FIBG_BOVIN | P12799 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:47
                                    35        45        55        65       
           FIBG_BOVIN    26 VATRDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLRTLEGILY  72
               SCOP domains d1jy2s_ S: Fibrinogen gamma chain               SCOP domains
               CATH domains 1jy2S00 S:2-48                                  CATH domains
           Pfam domains (1) -Fib_alpha-1jy2S01 S:3-48                       Pfam domains (1)
           Pfam domains (2) -Fib_alpha-1jy2S02 S:3-48                       Pfam domains (2)
         Sec.struct. author ..........hhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1jy2 S   2 VATRDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLRTLEGILY  48
                                    11        21        31        41
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Fib_alpha] (17)

(-) Gene Ontology  (13, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain N,Q   (FIBA_BOVIN | P02672)
molecular function
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0051258    protein polymerization    The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.
    GO:0005577    fibrinogen complex    A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.

Chain O,R   (FIBB_BOVIN | P02676)
molecular function
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0051258    protein polymerization    The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.
    GO:0005577    fibrinogen complex    A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.

Chain P,S   (FIBG_BOVIN | P12799)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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: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:0051258    protein polymerization    The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.
    GO:0005577    fibrinogen complex    A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.

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  1jy2
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  FIBA_BOVIN | P02672
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  FIBB_BOVIN | P02676
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  FIBG_BOVIN | P12799
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 Related Entries

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

UniProtKB/Swiss-Prot
        FIBA_BOVIN | P02672: 1deq 1jy3 2baf 2jor
        FIBB_BOVIN | P02676: 1deq 1jy3 2z4e 3h32
        FIBG_BOVIN | P12799: 1deq 1jy3

(-) Related Entries Specified in the PDB File

1jy3 THE STRUCTURE OF BOVINE FIBRINOGEN FRAGMENT E5 WAS ALSO SOLVED IN AN ORTHORHOMBIC CRYSTAL FORM