8PTZ

Cryo-EM structure of human Elp123 in complex with tRNA, S-ethyl-CoA, 5'-deoxyadenosine and methionine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of the human Elongator complex at work.

Abbassi, N.E.Jaciuk, M.Scherf, D.Bohnert, P.Rau, A.Hammermeister, A.Rawski, M.Indyka, P.Wazny, G.Chramiec-Glabik, A.Dobosz, D.Skupien-Rabian, B.Jankowska, U.Rappsilber, J.Schaffrath, R.Lin, T.Y.Glatt, S.

(2024) Nat Commun 15: 4094-4094

  • DOI: https://doi.org/10.1038/s41467-024-48251-y
  • Primary Citation of Related Structures:  
    8PTX, 8PTY, 8PTZ, 8PU0

  • PubMed Abstract: 

    tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cm 5 U 34 ) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structures of human ELP123 in complex with tRNA and cofactors at four different stages of the reaction. The structures at resolutions of up to 2.9 Å together with complementary functional analyses reveal the molecular mechanism of the modification reaction. Our results show that tRNA binding exposes a universally conserved uridine at position 33 (U 33 ), which triggers acetyl-CoA hydrolysis. We identify a series of conserved residues that are crucial for the radical-based acetylation of U 34 and profile the molecular effects of patient-derived mutations. Together, we provide the high-resolution view of human Elongator and reveal its detailed mechanism of action.


  • Organizational Affiliation

    Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 11,332Homo sapiensMutation(s): 0 
Gene Names: ELP1IKAPIKBKAP
UniProt & NIH Common Fund Data Resources
Find proteins for O95163 (Homo sapiens)
Explore O95163 
Go to UniProtKB:  O95163
PHAROS:  O95163
GTEx:  ENSG00000070061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95163
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 2826Homo sapiensMutation(s): 0 
Gene Names: ELP2STATIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IA86 (Homo sapiens)
Explore Q6IA86 
Go to UniProtKB:  Q6IA86
PHAROS:  Q6IA86
GTEx:  ENSG00000134759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IA86
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongator complex protein 3581Homo sapiensMutation(s): 0 
Gene Names: ELP3
EC: 2.3.1 (PDB Primary Data), 2.3.1.311 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9T3 (Homo sapiens)
Explore Q9H9T3 
Go to UniProtKB:  Q9H9T3
PHAROS:  Q9H9T3
GTEx:  ENSG00000134014 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9T3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
tRNA GlnD [auth X]75Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2U (Subject of Investigation/LOI)
Query on A2U

Download Ideal Coordinates CCD File 
G [auth C]S-Ethyl-CoA
C23 H40 N7 O16 P3 S
YGTAAWZKDDQUQN-RJFKWGFDSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
E [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
5AD (Subject of Investigation/LOI)
Query on 5AD

Download Ideal Coordinates CCD File 
F [auth C]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
MET (Subject of Investigation/LOI)
Query on MET

Download Ideal Coordinates CCD File 
H [auth C]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth X],
J [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101001394

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references