1hbh: Difference between revisions

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<StructureSection load='1hbh' size='340' side='right'caption='[[1hbh]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1hbh' size='340' side='right'caption='[[1hbh]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1hbh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Emerald_rockcod Emerald rockcod]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HBH FirstGlance]. <br>
<table><tr><td colspan='2'>[[1hbh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trematomus_bernacchii Trematomus bernacchii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HBH FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1hbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hbh OCA], [https://pdbe.org/1hbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hbh RCSB], [https://www.ebi.ac.uk/pdbsum/1hbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hbh ProSAT]</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=1hbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hbh OCA], [https://pdbe.org/1hbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hbh RCSB], [https://www.ebi.ac.uk/pdbsum/1hbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hbh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/HBA_TREBE HBA_TREBE]] Involved in oxygen transport from gills to the various peripheral tissues. [[https://www.uniprot.org/uniprot/HBB_TREBE HBB_TREBE]] Involved in oxygen transport from gills to the various peripheral tissues.  
[https://www.uniprot.org/uniprot/HBA_TREBE HBA_TREBE] Involved in oxygen transport from gills to the various peripheral tissues.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1hbh 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=1hbh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have determined the structure of deoxyhaemoglobin from the antarctic fish Pagothenia bernacchii at pH 6.2 to a resolution of 2.2 A with X-ray data from a twinned crystal deconvoluted so as to approximate data from a single crystal. The R-factor between the (twinned) model and the observed data is 16% for reflections used in refinement and 22% for reflections not used in refinement. The T (deoxy) structure was compared with the R (liganded) structure at pH 8.0 in an attempt to understand the structural basis of the greater affinity for hydrogen ions of T, relative to R, that comprises the Root effect. Up to half of the effect can be attributed to interaction of the residues Asp95 (G1)alpha and Asp101 (G3)beta: in R the residues are far apart and their carboxyl groups are unprotonated, but the shift at the alpha 1 beta 2 interface that accompanies the R to T transition brings them so close that they appear to share a proton between them. The proximity of Asp99 (G1)beta may contribute to the required raising of the pKa values of the other two Asp residues. These and neighbouring residues are sufficiently conserved in the haemoglobins of trout (component IV), carp and bluefin tuna, all of which exhibit the Root effect, for the same mechanism to apply. However, the environment is equally conserved in haemoglobins of Trematomus newnesi (major component) and trout (component I), which do not exhibit the Root effect, so that the structural factors controlling the Asp-Asp interaction remain unclear. No other residue appears to undergo an R to T change in the immediate neighbourhoods that could account for any significant portion of the Root effect, so at least half of the effect must result either from long-range electrostatic interactions or from a large number of local interactions.
Structure of deoxyhaemoglobin of the antarctic fish Pagothenia bernacchii with an analysis of the structural basis of the root effect by comparison of the liganded and unliganded haemoglobin structures.,Ito N, Komiyama NH, Fermi G J Mol Biol. 1995 Jul 28;250(5):648-58. PMID:7623382<ref>PMID:7623382</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1hbh" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Emerald rockcod]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fermi, G]]
[[Category: Trematomus bernacchii]]
[[Category: Ito, N]]
[[Category: Fermi G]]
[[Category: Komiyama, N H]]
[[Category: Ito N]]
[[Category: Oxygen carrier]]
[[Category: Komiyama NH]]

Revision as of 14:30, 27 March 2024

STRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII AND STRUCTURAL BASIS OF THE ROOT EFFECTSTRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII AND STRUCTURAL BASIS OF THE ROOT EFFECT

Structural highlights

1hbh is a 4 chain structure with sequence from Trematomus bernacchii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HBA_TREBE Involved in oxygen transport from gills to the various peripheral tissues.

Evolutionary Conservation

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

See Also

1hbh, resolution 2.20Å

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