8PTX

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

PDB DOI: https://doi.org/10.2210/pdb8PTX/pdb
EM Map EMD-17924: EMDB EMDataResource
NAKB: 8PTX

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-07-16 Released: 2024-04-17
Deposition Author(s): Abbassi, N., Jaciuk, M., Lin, T.-Y., Glatt, S.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Abbassi, N., Jaciuk, M., Lin, T.-Y., Glatt, S.

To be published.

Macromolecule Content

Total Structure Weight: 484.9 kDa
Atom Count: 24,378
Modelled Residue Count: 2,926
Deposited Residue Count: 4,146
Unique protein chains: 3
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 1	A, D	1,332	Homo sapiens	Mutation(s): 0 Gene Names: ELP1, IKAP, IKBKAP
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95163
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 2	B	826	Homo sapiens	Mutation(s): 0 Gene Names: ELP2, STATIP1
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IA86
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 3	C	581	Homo sapiens	Mutation(s): 0 Gene Names: ELP3 EC: 2.3.1
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H9T3
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
tRNA Gln	E [auth X]	75	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C]	H [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C]	F [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
5AD (Subject of Investigation/LOI) Query on 5AD Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C]	G [auth C]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
MET (Subject of Investigation/LOI) Query on MET Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C]	I [auth C]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth X] SDF format, chain K [auth X] SDF format, chain L [auth X] SDF format, chain M [auth X] MOL2 format, chain J [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] MOL2 format, chain M [auth X]	J [auth X], K [auth X], L [auth X], M [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Interactions & Density Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X]