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TitleIntegrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 2697, Year 2019
Publish dateJun 19, 2019
AuthorsDiego F Gauto / Leandro F Estrozi / Charles D Schwieters / Gregory Effantin / Pavel Macek / Remy Sounier / Astrid C Sivertsen / Elena Schmidt / Rime Kerfah / Guillaume Mas / Jacques-Philippe Colletier / Peter Güntert / Adrien Favier / Guy Schoehn / Paul Schanda / Jerome Boisbouvier /
PubMed AbstractAtomic-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 ...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 (<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 Å 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 Å 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.
External linksNat Commun / PubMed:31217444 / PubMed Central
MethodsEM (single particle) / NMR (solution) / NMR (solid-state)
Resolution4.1 Å
Structure data

4179

6f3k

6r8n

EMDB-4179, PDB-6f3k:
Combined solid-state NMR, solution-state NMR and EM data for structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii
PDB-6r8n: STRUCTURE DETERMINATION OF THE TETRAHEDRAL AMINOPEPTIDASE TET2 FROM P. HORIKOSHII BY USE OF COMBINED SOLID-STATE NMR, SOLUTION-STATE NMR AND EM DATA 4.1 A, FOLLOWED BY REAL_SPACE_REFINEMENT AT 4.1 A
Method: EM (single particle) / Resolution: 4.1 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • Pyrococcus horikoshii (archaea)
  • pyrococcus horikoshii (strain atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / ot-3) (archaea)
  • pyrococcus horikoshii ot3 (archaea)
KeywordsPEPTIDE BINDING PROTEIN / peptidase / protein quality control / oligomer / aminopeptidase

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