Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration, microscopy

Macromolecule Content

• Total Structure Weight: 39.2 kDa 
• Atom Count: 2,751 
• Modelled Residue Count: 353 
• Deposited Residue Count: 353 
• Unique protein chains: 1

 6F3K

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

• PDB DOI:  https://doi.org/10.2210/pdb6F3K/pdb
• BMRB: 27211
• EM Map EMD-4179: EMDB EMDataResource

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-28 Released: 2018-03-14 
• Deposition Author(s): 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.
• Funding Organization(s): European Research Council, French National Research Agency

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Experimental Data Snapshot

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

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• Method: SOLUTION NMR
• Conformers Submitted: 10 

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

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

• PubMed: 31217444 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrahedral aminopeptidase	A	353	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: frvX, PH1527 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	X-PLOR	4.39

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
European Research Council		311318
French National Research Agency	France	ANR-10-INSB-05-02
French National Research Agency	France	ANR-10-LABX-49-01

Revision History  

• 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