1v5h

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Human Cytoglobin (Ferric Form)

Structural highlights

1v5h is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

CYGB_HUMAN May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Cytoglobin (Cgb), a newly discovered member of the vertebrate globin family, binds O(2) reversibly via its heme, as is the case for other mammalian globins (hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb)). While Cgb is expressed in various tissues, its physiological role is not clearly understood. Here, the X-ray crystal structure of wild type human Cgb in the ferric state at 2.4A resolution is reported. In the crystal structure, ferric Cgb is dimerized through two intermolecular disulfide bonds between Cys38(B2) and Cys83(E9), and the dimerization interface is similar to that of lamprey Hb and Ngb. The overall backbone structure of the Cgb monomer exhibits a traditional globin fold with a three-over-three alpha-helical sandwich, in which the arrangement of helices is basically the same among all globins studied to date. A detailed comparison reveals that the backbone structure of the CD corner to D helix region, the N terminus of the E-helix and the F-helix of Cgb resembles more closely those of pentacoordinated globins (Mb, lamprey Hb), rather than hexacoordinated globins (Ngb, rice Hb). However, the His81(E7) imidazole group coordinates directly to the heme iron as a sixth axial ligand to form a hexcoordinated heme, like Ngb and rice Hb. The position and orientation of the highly conserved residues in the heme pocket (Phe(CD1), Val(E11), distal His(E7) and proximal His(F8)) are similar to those of other globin proteins. Two alternative conformations of the Arg84(E10) guanidium group were observed, suggesting that it participates in ligand binding to Cgb, as is the case for Arg(E10) of Aplysia Mb and Lys(E10) of Ngb. The structural diversities and similarities among globin proteins are discussed with relevance to molecular evolutionary relationships.

Structural basis of human cytoglobin for ligand binding.,Sugimoto H, Makino M, Sawai H, Kawada N, Yoshizato K, Shiro Y J Mol Biol. 2004 Jun 11;339(4):873-85. PMID:15165856^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sugimoto H, Makino M, Sawai H, Kawada N, Yoshizato K, Shiro Y. Structural basis of human cytoglobin for ligand binding. J Mol Biol. 2004 Jun 11;339(4):873-85. PMID:15165856 doi:10.1016/j.jmb.2004.04.024

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v5h"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Human Cytoglobin (Ferric Form)==
-<StructureSection load='1v5h' size='340' side='right' caption='[[1v5h]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1v5h' size='340' side='right'caption='[[1v5h]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v5h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V5H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V5H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v5h]] is a 1 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=1V5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V5H FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><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]] 2.4&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYGB, STAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v5h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v5h RCSB], [http://www.ebi.ac.uk/pdbsum/1v5h PDBsum], [http://www.topsan.org/Proteins/RSGI/1v5h TOPSAN]</span></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=1v5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v5h OCA], [https://pdbe.org/1v5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v5h RCSB], [https://www.ebi.ac.uk/pdbsum/1v5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v5h ProSAT], [https://www.topsan.org/Proteins/RSGI/1v5h TOPSAN]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYGB_HUMAN CYGB_HUMAN] May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.
 == 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/v5/1v5h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v5/1v5h_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1v5h ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1v5h" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 34: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Kawada, N.]]
+[[Category: Large Structures]]
-[[Category: Makino, M.]]
+[[Category: Kawada N]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Makino M]]
-[[Category: Sawai, H.]]
+[[Category: Sawai H]]
-[[Category: Shiro, Y.]]
+[[Category: Shiro Y]]
-[[Category: Sugimoto, H.]]
+[[Category: Sugimoto H]]
-[[Category: Yoshizato, K.]]
+[[Category: Yoshizato K]]
-[[Category: Globin]]
-[[Category: Heme]]
-[[Category: Ligand binding]]
-[[Category: Oxygen storage]]
-[[Category: Oxygen storage-transport complex]]
-[[Category: Oxygen transport]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]

1v5h

From Proteopedia

Current revision

Crystal Structure of Human Cytoglobin (Ferric Form)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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