6QK7 | pdb_00006qk7

Elongator catalytic subcomplex Elp123 lobe

PDB DOI: https://doi.org/10.2210/pdb6QK7/pdb
EM Map EMD-4571: EMDB EMDataResource

Classification: TRANSLATION
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2019-01-28 Released: 2019-07-17
Deposition Author(s): Dauden, M.I., Jaciuk, M., Glatt, S.
Funding Organization(s): German Research Foundation, Polish National Science Centre

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

PubMed: 31309145 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aaw2326
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 460.21 kDa
Atom Count: 20,790
Modeled Residue Count: 2,592
Deposited Residue Count: 4,043
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 1	A, D	1,349	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06706 Go to UniProtKB: Q06706
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06706
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 2	B	788	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P42935 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42935 Go to UniProtKB: P42935
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42935
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 3	C	557	Saccharomyces cerevisiae S288C	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02908
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
5AD Query on 5AD Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	RSRef
RECONSTRUCTION	RELION	2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Dauden, M.I.

Jaciuk, M.

Glatt, S.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	BR921/9-1 & Mu3173/2-1
Polish National Science Centre	Poland	UMO-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