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3w3a

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Current revision (08:43, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3w3a' size='340' side='right'caption='[[3w3a]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
<StructureSection load='3w3a' size='340' side='right'caption='[[3w3a]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3w3a]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W3A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3w3a]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W3A FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a5c|3a5c]], [[3a5d|3a5d]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3w3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w3a OCA], [https://pdbe.org/3w3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w3a RCSB], [https://www.ebi.ac.uk/pdbsum/3w3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w3a 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=3w3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w3a OCA], [https://pdbe.org/3w3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w3a RCSB], [https://www.ebi.ac.uk/pdbsum/3w3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w3a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/VATF_THET8 VATF_THET8]] Produces ATP from ADP in the presence of a proton gradient across the membrane. [[https://www.uniprot.org/uniprot/VATA_THET8 VATA_THET8]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit. [[https://www.uniprot.org/uniprot/VATD_THET8 VATD_THET8]] Produces ATP from ADP in the presence of a proton gradient across the membrane. [[https://www.uniprot.org/uniprot/VATB_THET8 VATB_THET8]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit.
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[https://www.uniprot.org/uniprot/VATA_THET8 VATA_THET8] Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases. Here, we report a complete model of the extra-membrane domain of the V-ATPase (V1-ATPase) of a thermophilic bacterium, Thermus thermophilus, consisting of three A subunits, three B subunits, one D subunit, and one F subunit. The X-ray structure at 3.9A resolution provides detailed information about the interactions between A3B3 and DF subcomplexes as well as interactions among the respective subunits, which are defined by the properties of side chains. Asymmetry at the intersubunit interfaces was detected from the structural differences among the three AB pairs in the different reaction states, while the large interdomain motion in the catalytic A subunits was not observed unlike F1 from various species and V1 from Enterococcus hirae. Asymmetry is mainly realized by rigid-body rearrangements of the relative position between A and B subunits. This is consistent with the previous observations by the high-resolution electron microscopy for the whole V-ATPase complexes. Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits.
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Origin of Asymmetry at the Intersubunit Interfaces of V-ATPase from Thermusthermophilus.,Nagamatsu Y, Takeda K, Kuranaga T, Numoto N, Miki K J Mol Biol. 2013 Apr 29. pii: S0022-2836(13)00270-2. doi:, 10.1016/j.jmb.2013.04.022. PMID:23639357<ref>PMID:23639357</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3w3a" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[ATPase 3D structures|ATPase 3D structures]]
*[[ATPase 3D structures|ATPase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thermus thermophilus]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Kuranaga, T]]
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[[Category: Kuranaga T]]
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[[Category: Miki, K]]
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[[Category: Miki K]]
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[[Category: Nagamatsu, Y]]
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[[Category: Nagamatsu Y]]
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[[Category: Numoto, N]]
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[[Category: Numoto N]]
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[[Category: Takeda, K]]
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[[Category: Takeda K]]
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[[Category: Atp synthesis]]
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[[Category: Catalytic domain]]
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[[Category: Hydrogen ion transport]]
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[[Category: Hydrolase]]
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[[Category: Hydrolysis]]
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[[Category: Molecular motor protein]]
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[[Category: Nucleotide-binding]]
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[[Category: Proton-translocating atpase]]
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[[Category: Quaternary]]
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[[Category: Vacuolar proton-translocating atpase]]
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Current revision

Crystal structure of V1-ATPase at 3.9 angstrom resolution

PDB ID 3w3a

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