6F3K

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

  • Method: SOLUTION NMR
  • Conformers Submitted: 10 

  • Method: SOLID-STATE NMR
  • Conformers Submitted: 10 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.

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.

(2019) Nat Commun 10: 2697-2697

  • DOI: https://doi.org/10.1038/s41467-019-10490-9
  • Primary Citation of Related Structures:  
    6F3K, 6R8N

  • 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.


  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France. leandro.estrozi@ibs.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrahedral aminopeptidase353Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: frvXPH1527
EC: 3.4.11
UniProt
Find proteins for O59196 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59196 
Go to UniProtKB:  O59196
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59196
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
  • Method: SOLUTION NMR
  • Conformers Submitted: 10 
  • Method: SOLID-STATE NMR
  • Conformers Submitted: 10 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTX-PLOR4.39

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council311318
French National Research AgencyFranceANR-10-INSB-05-02
French National Research AgencyFranceANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-08-21
    Changes: Data collection
  • Version 1.3: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations