1fzc: Difference between revisions

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-{{Seed}}
-[[Image:1fzc.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS==
-The line below this paragraph, containing "STRUCTURE_1fzc", creates the "Structure Box" on the page.
+<StructureSection load='1fzc' size='340' side='right'caption='[[1fzc]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1fzc]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The November 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Fibrin''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_11 10.2210/rcsb_pdb/mom_2006_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_1fzc|  PDB=1fzc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzc OCA], [https://pdbe.org/1fzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzc RCSB], [https://www.ebi.ac.uk/pdbsum/1fzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzc ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/FIBA_HUMAN FIBA_HUMAN] Defects in FGA are a cause of congenital afibrinogenemia (CAFBN) [MIM:[https://omim.org/entry/202400 202400]. This is a rare autosomal recessive disorder characterized by bleeding that varies from mild to severe and by complete absence or extremely low levels of plasma and platelet fibrinogen. Note=The majority of cases of afibrinogenemia are due to truncating mutations. Variations in position Arg-35 (the site of cleavage of fibrinopeptide a by thrombin) leads to alpha-dysfibrinogenemias.  Defects in FGA are a cause of amyloidosis type 8 (AMYL8) [MIM:[https://omim.org/entry/105200 105200]; also known as systemic non-neuropathic amyloidosis or Ostertag-type amyloidosis. AMYL8 is a hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash.<ref>PMID:8097946</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/FIBA_HUMAN FIBA_HUMAN] Fibrinogen has a double function: yielding monomers that polymerize into fibrin and acting as a cofactor in platelet aggregation.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fz/1fzc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1fzc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Factor XIII-cross-linked fragment D (double-D) from human fibrin was crystallized in the presence of two different peptide ligands and the X-ray structure determined at 2.3 A. The peptide Gly-Pro-Arg-Pro-amide, which is an analogue of the knob exposed by the thrombin-catalyzed removal of fibrinopeptide A, was found to reside in the gamma-chain holes, and the peptide Gly-His-Arg-Pro-amide, which corresponds to the beta-chain knob, was found in the homologous beta-chain holes. The structure shows for the first time that the beta-chain knob does indeed bind to a homologous hole on the beta-chain. The gamma- and beta-chain holes are structurally very similar, and it is remarkable they are able to distinguish between these two peptides that differ by a single amino acid. Additionally, we have found that the beta-chain domain, like its gamma-chain counterpart, binds calcium.
-===CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS===
+Crystal structure of fragment double-D from human fibrin with two different bound ligands.,Everse SJ, Spraggon G, Veerapandian L, Riley M, Doolittle RF Biochemistry. 1998 Jun 16;37(24):8637-42. PMID:9628725<ref>PMID:9628725</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1fzc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9628725}}, adds the Publication Abstract to the page
+*[[Fibrin|Fibrin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9628725 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9628725}}
+__TOC__
+</StructureSection>
-==About this Structure==
-FZC is a 10 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The November 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Fibrin''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_11 10.2210/rcsb_pdb/mom_2006_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZC OCA].
-==Reference==
-<ref group="xtra">PMID:9628725</ref><references group="xtra"/>
 [[Category: Fibrin]]
 [[Category: Homo sapiens]]
-[[Category: Doolittle, R F.]]
+[[Category: Large Structures]]
-[[Category: Everse, S J.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Riley, M.]]
+[[Category: Doolittle RF]]
-[[Category: Spraggon, G.]]
+[[Category: Everse SJ]]
-[[Category: Veerapandian, L.]]
+[[Category: Riley M]]
-[[Category: Blood coagulation]]
+[[Category: Spraggon G]]
-[[Category: Crosslinking]]
+[[Category: Veerapandian L]]
-[[Category: Plasma protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:46:29 2009''