3rfu: Difference between revisions

Latest revision as of 10:11, 13 August 2026

Crystal structure of a copper-transporting PIB-type ATPase

Structural highlights

3rfu is a 4 chain structure with sequence from Legionella pneumophila subsp. pneumophila str. Philadelphia 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Ligands:	ALF, K, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

COPA_LEGPH Couples the hydrolysis of ATP with the export of copper.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 A resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B proteins associated with Menkes' and Wilson's diseases.

Crystal structure of a copper-transporting PIB-type ATPase.,Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286^[4]

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

References

↑ Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721
↑ Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu(+) transport ATPase. The activation by Cu(+) and ATP. Biochim Biophys Acta Biomembr. 2022 Feb 1;1864(2):183822. PMID:34826402 doi:10.1016/j.bbamem.2021.183822
↑ Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191
↑ Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721

[2] Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu(+) transport ATPase. The activation by Cu(+) and ATP. Biochim Biophys Acta Biomembr. 2022 Feb 1;1864(2):183822. PMID:34826402 doi:10.1016/j.bbamem.2021.183822

[3] Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191

[4] Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 3rfu is ON HOLD
+==Crystal structure of a copper-transporting PIB-type ATPase==
+<StructureSection load='3rfu' size='340' side='right'caption='[[3rfu]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3rfu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._Philadelphia_1 Legionella pneumophila subsp. pneumophila str. Philadelphia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFU 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]] 3.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3rfu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfu OCA], [https://pdbe.org/3rfu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rfu RCSB], [https://www.ebi.ac.uk/pdbsum/3rfu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COPA_LEGPH COPA_LEGPH] Couples the hydrolysis of ATP with the export of copper.<ref>PMID:24317491</ref> <ref>PMID:34826402</ref> <ref>PMID:21716286</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 A resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B proteins associated with Menkes' and Wilson's diseases.
-Authors: Gourdon, P., Liu, X. , Skjorringe, T., Morth, J.P., Birk Moller, L., Panyella Pedersen, B., Nissen, P.
+Crystal structure of a copper-transporting PIB-type ATPase.,Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286<ref>PMID:21716286</ref>
-Description: Crystal structure
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3rfu" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[ATPase 3D structures|ATPase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Legionella pneumophila subsp. pneumophila str. Philadelphia 1]]
+[[Category: Birk Moller L]]
+[[Category: Gourdon P]]
+[[Category: Liu X]]
+[[Category: Morth JP]]
+[[Category: Nissen P]]
+[[Category: Panyella Pedersen B]]
+[[Category: Skjorringe T]]

3rfu: Difference between revisions

Latest revision as of 10:11, 13 August 2026

Crystal structure of a copper-transporting PIB-type ATPase

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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