6QK7

Elongator catalytic subcomplex Elp123 lobe


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8ASV 8ASW 8AVG


Literature

Molecular basis of tRNA recognition by the Elongator complex.

Dauden, M.I.Jaciuk, M.Weis, F.Lin, T.Y.Kleindienst, C.Abbassi, N.E.H.Khatter, H.Krutyholowa, R.Breunig, K.D.Kosinski, J.Muller, C.W.Glatt, S.

(2019) Sci Adv 5: eaaw2326-eaaw2326

  • DOI: https://doi.org/10.1126/sciadv.aaw2326
  • Primary Citation of Related Structures:  
    6QK7

  • PubMed Abstract: 

    The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 1
A, D
1,349Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06706 
Go to UniProtKB:  Q06706
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06706
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 2788Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P42935 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42935 
Go to UniProtKB:  P42935
Entity Groups  
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UniProt GroupP42935
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 3557Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.1.48 (PDB Primary Data), 2.3.1.311 (UniProt)
UniProt
Find proteins for Q02908 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02908 
Go to UniProtKB:  Q02908
Entity Groups  
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UniProt GroupQ02908
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRSRef
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyBR921/9-1 & Mu3173/2-1
Polish National Science CentrePolandUMO-2015/19/B/NZ1/00343

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Refinement description