1rf1: Difference between revisions
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|PDB= 1rf1 |SIZE=350|CAPTION= <scene name='initialview01'>1rf1</scene>, resolution 2.53Å | |PDB= 1rf1 |SIZE=350|CAPTION= <scene name='initialview01'>1rf1</scene>, resolution 2.53Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= FGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), FGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), FGG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= FGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), FGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), FGG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1lt9|1LT9]], [[1ltj|1LTJ]], [[1re3|1RE3]], [[1re4|1RE4]], [[1fzc|1FZC]], [[1fzg|1FZG]], [[1rf0|1RF0]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rf1 OCA], [http://www.ebi.ac.uk/pdbsum/1rf1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rf1 RCSB]</span> | |||
}} | }} | ||
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==Disease== | ==Disease== | ||
Known | Known disease associated with this structure: Afibrinogenemia, congenital OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134820 134820]], Amyloidosis, hereditary renal OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134820 134820]], Dysfibrinogenemia, alpha type, causing bleeding diathesis OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134820 134820]], Dysfibrinogenemia, alpha type, causing recurrent thrombosis OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134820 134820]], Afibrinogenemia, congenital OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134830 134830]], Dysfibrinogenemia, beta type OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134830 134830]], Thrombophilia, dysfibrinogenemic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134830 134830]], Dysfibrinogenemia, gamma type OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134850 134850]], Hypofibrinogenemia, gamma type OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134850 134850]], Thrombophilia, dysfibrinogenemic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134850 134850]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Kostelansky, M S.]] | [[Category: Kostelansky, M S.]] | ||
[[Category: Lord, S T.]] | [[Category: Lord, S T.]] | ||
[[Category: blood coagulation]] | [[Category: blood coagulation]] | ||
[[Category: fibrinogen]] | [[Category: fibrinogen]] | ||
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[[Category: recombinant fibrinogen fragment d]] | [[Category: recombinant fibrinogen fragment d]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:27:13 2008'' | ||
Revision as of 23:27, 30 March 2008
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| , resolution 2.53Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | FGA (Homo sapiens), FGB (Homo sapiens), FGG (Homo sapiens) | ||||||
| Related: | 1LT9, 1LTJ, 1RE3, 1RE4, 1FZC, 1FZG, 1RF0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide
OverviewOverview
Structural analysis of recombinant fibrinogen fragment D revealed that the calcium-binding site (beta2-site) composed of residues BbetaAsp261, BbetaAsp398, BbetaGly263, and gammaGlu132 is modulated by the "B:b" interaction. To determine the beta2-site's role in polymerization, we engineered variant fibrinogen gammaE132A in which calcium binding to the beta2-site was disrupted by replacing glutamic acid at gamma132 with alanine. We compared polymerization of gammaE132A to normal fibrinogen as a function of calcium concentration. Polymerization of gammaE132A at concentrations of calcium <or=1 mM exhibited an uncharacteristic 2-3-fold increase in lateral aggregation and fiber thickness compared to normal fibrinogen, while polymerization of variant and normal were indistinguishable at 10 mM calcium. These results suggest that the beta2-site controls the extent of lateral aggregation. That is, when the calcium anchor (beta2-site) is eliminated before "B:b" interactions occur then lateral aggregation is enhanced. We solved structures of fragment D of gammaE132A fibrinogen (rfD-gammaE132A) with and without Gly-His-Arg-Pro-amide (GHRPam) and found no change to the global structure. X-ray diffraction data showed GHRPam binding in the "a" and "b" polymerization sites and that calcium could still bind to the beta2-site of gammaE132A fibrinogen at 70 mM calcium. We found that the gamma2 calcium-binding site (in loop gamma294-301) did not have calcium bound in the structure of fragment D of gammaE132A fibrinogen with GHRPam bound (rfD-gammaE132A+GH). Analysis of structures rfD-gammaE132A+GH and rfD-BbetaD398A+GH indicated that differences in calcium occupation of the gamma2-site resulted from minor conformational changes provoked by crystal packing and GHRPam binding to the "a" site did not directly modulate calcium binding to this site.
DiseaseDisease
Known disease associated with this structure: Afibrinogenemia, congenital OMIM:[134820], Amyloidosis, hereditary renal OMIM:[134820], Dysfibrinogenemia, alpha type, causing bleeding diathesis OMIM:[134820], Dysfibrinogenemia, alpha type, causing recurrent thrombosis OMIM:[134820], Afibrinogenemia, congenital OMIM:[134830], Dysfibrinogenemia, beta type OMIM:[134830], Thrombophilia, dysfibrinogenemic OMIM:[134830], Dysfibrinogenemia, gamma type OMIM:[134850], Hypofibrinogenemia, gamma type OMIM:[134850], Thrombophilia, dysfibrinogenemic OMIM:[134850]
About this StructureAbout this Structure
1RF1 is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Calcium-binding site beta 2, adjacent to the "b" polymerization site, modulates lateral aggregation of protofibrils during fibrin polymerization., Kostelansky MS, Lounes KC, Ping LF, Dickerson SK, Gorkun OV, Lord ST, Biochemistry. 2004 Mar 9;43(9):2475-83. PMID:14992585
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