6F3K

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

Summary for 6F3K

• Entry DOI: 10.2210/pdb6f3k/pdb
• EMDB information: 4179
• NMR Information: BMRB: 27211
• Descriptor: Tetrahedral aminopeptidase, ZINC ION (2 entities in total)
• Functional Keywords: peptidase, protein quality control, oligomer, aminopeptidase, peptide binding protein
• Biological source: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
• Total number of polymer chains: 1
• Total formula weight: 39201.85

Authors

Gauto, D.F.,Estrozi, L.F.,Schwieters, C.D.,Effantin, G.,Macek, P.,Sounier, R.,Kerfah, R.,Sivertsen, A.C.,Colletier, J.P.,Boisbouvier, J.,Schoehn, G.,Favier, A.,Schanda, P. (deposition date: 2017-11-28, release date: 2018-03-14, Last modification date: 2023-09-13)

Primary citation

Gauto, D.F.,Estrozi, L.F.,Schwieters, C.D.,Effantin, G.,Macek, P.,Sounier, R.,Sivertsen, A.C.,Schmidt, E.,Kerfah, R.,Mas, G.,Colletier, J.P.,Guntert, P.,Favier, A.,Schoehn, G.,Schanda, P.,Boisbouvier, J.
Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.
Nat Commun, 10:2697-2697, 2019

PubMed Abstract: 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.

PubMed: 31217444
DOI: 10.1038/s41467-019-10490-9

Experimental method

ELECTRON MICROSCOPY (4.1 Å)
SOLID-STATE NMR (4.1 Å)
SOLUTION NMR (4.1 Å)