6QK7

Elongator catalytic subcomplex Elp123 lobe

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 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 ...

    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: 

    Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongator complex protein 1A, D1,349Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IKI3, ELP1, TOT1, YLR384C, L3502.7
UniProt
Find proteins for Q06706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06706 
Go to UniProtKB:  Q06706
Entity Groups  
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UniProt GroupQ06706
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongator complex protein 2B788Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ELP2, TOT2, YGR200C, G7725
UniProt
Find proteins for P42935 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P42935 
Go to UniProtKB:  P42935
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UniProt GroupP42935
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongator complex protein 3C557Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ELP3, HPA1, TOT3, YPL086C
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
E [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
5AD
Query on 5AD
Download Ideal Coordinates CCD File 
F [auth C]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N		 Ligand Interaction
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



View more in-depth experimental data
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