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NMR Structure - model 1  (Jmol Viewer)
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(-) Description

Authors :  M. Hoshino, Y. Hagihara, I. Nishii, T. Yamazaki, H. Kato, Y. Goto
Date :  27 Oct 00  (Deposition) - 15 Nov 00  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Short Consensus Repeat, Sushi-Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. Hoshino, Y. Hagihara, I. Nishii, T. Yamazaki, H. Kato, Y. Goto
Identification Of The Phospholipid-Binding Site Of Human Beta(2)-Glycoprotein I Domain V By Heteronuclear Magnetic Resonance.
J. Mol. Biol. V. 304 927 2000
PubMed-ID: 11124037  |  Reference-DOI: 10.1006/JMBI.2000.4243
(for further references see the PDB file header)

(-) Compounds

    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1G4F)

(-) Sites  (0, 0)

(no "Site" information available for 1G4F)

(-) SS Bonds  (3, 3)

NMR Structure
1A:5 -A:56
2A:41 -A:66
3A:48 -A:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G4F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G4F)

(-) Exons   (3, 3)

NMR Structure (3, 3)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

NMR Structure
   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:86
 aligned with APOH_HUMAN | P02749 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:86
                                   269       279       289       299       309       319       329       339      
               SCOP domains d1g4fa_ A: beta2-glycoprotein I                                                        SCOP domains
               CATH domains 1g4fA00 A:1-86 Complement Module, domain 1                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------L----------------------------------------------------------G---------S---------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.6-----------------------------------------------------------------Exon 1.8           Transcript 1 (1)
           Transcript 1 (2) --Exon 1.7  PDB: A:3-69 UniProt: 262-328                             ----------------- Transcript 1 (2)
                                    10        20        30        40        50        60        70        80      

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G4F)

(-) Gene Ontology  (39, 39)

NMR Structure(hide GO term definitions)
Chain A   (APOH_HUMAN | P02749)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0060230    lipoprotein lipase activator activity    Binds to and increases the activity of a lipoprotein lipase, an enzyme that catalyzes of the hydrolysis of a lipid within a lipoprotein.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    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:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001937    negative regulation of endothelial cell proliferation    Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0033033    negative regulation of myeloid cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
    GO:0060268    negative regulation of respiratory burst    Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0034392    negative regulation of smooth muscle cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0051006    positive regulation of lipoprotein lipase activity    Any process that activates or increases the activity of the enzyme lipoprotein lipase.
    GO:0010898    positive regulation of triglyceride catabolic process    Any process that increases the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of triglyceride.
    GO:0030193    regulation of blood coagulation    Any process that modulates the frequency, rate or extent of blood coagulation.
    GO:0051917    regulation of fibrinolysis    Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0034014    response to triglyceride    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a triglyceride stimulus.
    GO:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
    GO:0034197    triglyceride transport    The directed movement of triglyceride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0042627    chylomicron    A large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    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:0031089    platelet dense granule lumen    The volume enclosed by the membrane of the platelet dense granule.
    GO:0034361    very-low-density lipoprotein particle    A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.


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 Related Entries

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

        APOH_HUMAN | P027491c1z 1g4g 1qub 2kri 3op8 4jhs

(-) Related Entries Specified in the PDB File