6f3k

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==Combined solid-state NMR, solution-state NMR and EM data for structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii==
==Combined solid-state NMR, solution-state NMR and EM data for structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii==
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<SX load='6f3k' size='340' side='right' viewer='molstar' caption='[[6f3k]], [[Resolution|resolution]] 4.10&Aring;, [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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<SX load='6f3k' size='340' side='right' viewer='molstar' caption='[[6f3k]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6f3k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F3K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6F3K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6f3k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F3K 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=ZN:ZINC+ION'>ZN</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">Electron Microscopy , Hybrid , Solid-state NMR , Solution NMR, [[Resolution|Resolution]] 4.1&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">frvX, PH1527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6f3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f3k OCA], [http://pdbe.org/6f3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f3k RCSB], [http://www.ebi.ac.uk/pdbsum/6f3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f3k ProSAT]</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=6f3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f3k OCA], [https://pdbe.org/6f3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f3k RCSB], [https://www.ebi.ac.uk/pdbsum/6f3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f3k ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/TET_PYRHO TET_PYRHO]] Functions as an aminopeptidase, with a clear preference for leucine as the N-terminal amino acid. However, can also cleave moderately long polypeptide substrates of various compositions in a fairly unspecific manner. Has neither carboxypeptidase nor endoproteolytic activities, and it is devoid of N-terminal deblocking activity. Is involved in protein degradation, performing degradation of oligopeptides produced by the proteasome into single amino acids.<ref>PMID:15375159</ref> <ref>PMID:15713475</ref> <ref>PMID:15736957</ref>
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[https://www.uniprot.org/uniprot/TET_PYRHO TET_PYRHO] Functions as an aminopeptidase, with a clear preference for leucine as the N-terminal amino acid. However, can also cleave moderately long polypeptide substrates of various compositions in a fairly unspecific manner. Has neither carboxypeptidase nor endoproteolytic activities, and it is devoid of N-terminal deblocking activity. Is involved in protein degradation, performing degradation of oligopeptides produced by the proteasome into single amino acids.<ref>PMID:15375159</ref> <ref>PMID:15713475</ref> <ref>PMID:15736957</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (&lt;30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 A by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 A resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.
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Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.,Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Guntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J Nat Commun. 2019 Jun 19;10(1):2697. doi: 10.1038/s41467-019-10490-9. PMID:31217444<ref>PMID:31217444</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 6f3k" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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</SX>
</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Pyrococcus horikoshii]]
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Boisbouvier, J]]
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[[Category: Boisbouvier J]]
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[[Category: Colletier, J P]]
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[[Category: Colletier JP]]
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[[Category: Effantin, G]]
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[[Category: Effantin G]]
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[[Category: Estrozi, L F]]
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[[Category: Estrozi LF]]
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[[Category: Favier, A]]
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[[Category: Favier A]]
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[[Category: Gauto, D F]]
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[[Category: Gauto DF]]
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[[Category: Kerfah, R]]
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[[Category: Kerfah R]]
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[[Category: Macek, P]]
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[[Category: Macek P]]
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[[Category: Schanda, P]]
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[[Category: Schanda P]]
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[[Category: Schoehn, G]]
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[[Category: Schoehn G]]
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[[Category: Schwieters, C D]]
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[[Category: Schwieters CD]]
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[[Category: Sivertsen, A C]]
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[[Category: Sivertsen AC]]
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[[Category: Sounier, R]]
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[[Category: Sounier R]]
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[[Category: Aminopeptidase]]
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[[Category: Oligomer]]
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[[Category: Peptidase]]
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[[Category: Peptide binding protein]]
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[[Category: Protein quality control]]
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Current revision

Combined solid-state NMR, solution-state NMR and EM data for structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii

6f3k, resolution 4.10Å

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