This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1fq3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:15, 27 March 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1fq3.gif|left|200px]]<br /><applet load="1fq3" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1fq3, resolution 3.1&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF HUMAN GRANZYME B'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF HUMAN GRANZYME B==
-
Granzyme B is the prototypic member of the granzymes, a family of trypsin-like serine proteinases localized in the dense cytoplasmic granules of activated natural killer cells and cytotoxic T lymphocytes. Granzyme B directly triggers apoptosis in target cells by activating the caspase pathway, and has been implicated in the etiology of rheumatoid arthritis. Human granzyme B expressed in a baculovirus system has been crystallized without inhibitor and its structure has been determined to 3.1 A resolution, after considerably improving the diffraction power of the crystals by controlled humidity changes. The granzyme B structure reveals an overall fold similar to that found in cathepsin G and human chymase. The guanidinium group of Arg226, anchored at the back of the S1-specificity pocket, can form a salt bridge with the P1-Asp side chain of a bound peptide substrate. The architecture of the substrate binding site of granzyme B appears to be designed to accommodate and cleave hexapeptides such as the sequence Ile-Glu-Thr-Asp-/Ser-Gly present in the activation site of pro-caspase-3, a proven physiological substrate of granzyme B. These granzyme B crystals, with fully accessible active sites, are well suited for soaking with small synthetic inhibitors that might be used for a treatment of chronic inflammatory disorders.
+
<StructureSection load='1fq3' size='340' side='right'caption='[[1fq3]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1fq3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FQ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FQ3 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fq3 OCA], [https://pdbe.org/1fq3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fq3 RCSB], [https://www.ebi.ac.uk/pdbsum/1fq3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fq3 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GRAB_HUMAN GRAB_HUMAN] This enzyme is necessary for target cell lysis in cell-mediated immune responses. It cleaves after Asp. Seems to be linked to an activation cascade of caspases (aspartate-specific cysteine proteases) responsible for apoptosis execution. Cleaves caspase-3, -7, -9 and 10 to give rise to active enzymes mediating apoptosis.
 +
== 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/fq/1fq3_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1fq3 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1FQ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Granzyme_B Granzyme B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.79 3.4.21.79] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FQ3 OCA].
+
*[[Granzyme|Granzyme]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of the caspase activator human granzyme B, a proteinase highly specific for an Asp-P1 residue., Estebanez-Perpina E, Fuentes-Prior P, Belorgey D, Braun M, Kiefersauer R, Maskos K, Huber R, Rubin H, Bode W, Biol Chem. 2000 Dec;381(12):1203-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11209755 11209755]
+
-
[[Category: Granzyme B]]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Belorgey, D.]]
+
[[Category: Belorgey D]]
-
[[Category: Bode, W.]]
+
[[Category: Bode W]]
-
[[Category: Estebanez-Perpina, E.]]
+
[[Category: Estebanez-Perpina E]]
-
[[Category: Fuentes-Prior, P.]]
+
[[Category: Fuentes-Prior P]]
-
[[Category: Rubin, H.]]
+
[[Category: Rubin H]]
-
[[Category: SO4]]
+
-
[[Category: chymotrypsin-like serine proteinase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:41:24 2008''
+

Current revision

CRYSTAL STRUCTURE OF HUMAN GRANZYME B

PDB ID 1fq3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1fq3"
Personal tools