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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-019-10490-9

  • 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, gene ...

    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.,Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France. paul.schanda@ibs.fr.,NMR-Bio, 5 Place Robert Schuman, F-38025, Grenoble, France.,Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,Biozentrum University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland.,Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.,Laboratory of Imaging Sciences, Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA.,Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan.,Institut de Génomique Fonctionnelle, CNRS UMR-5203, INSERM U1191, University of Montpellier, F-34000, Montpellier, France.,Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.,Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France. adrien.favier@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tetrahedral aminopeptidase
A, B, C, D, E, F, G, H, I, J, K, L
353Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: frvX
EC: 3.4.11.-
Find proteins for O59196 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59196
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 
  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE11-0018-01
French National Research AgencyFranceANR-10-INSB-05-02
French National Research AgencyFranceANR-10-LABX-49-01
European Research CouncilFranceStG-2012-311318-ProtDyn2Function
European Research CouncilFranceCoG-2010-260887
European Research CouncilFranceStG-311318

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection