8PU0

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

• PDB DOI: https://doi.org/10.2210/pdb8PU0/pdb
• EM Map EMD-17927: EMDB EMDataResource
• NAKB: 8PU0

• 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: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 484.73 kDa 
• Atom Count: 22,416 
• Modelled Residue Count: 2,682 
• Deposited Residue Count: 4,146 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongator complex protein 1	A, D [auth E]	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 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 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 ID: 4
Molecule	Chains	Length	Organism	Image
tRNA Gln	E [auth X]	75	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCA (Subject of Investigation/LOI)	F [auth C]	DESULFO-COENZYME A C21 H36 N7 O16 P3 ILWZMFJBPIYQKW-IBOSZNHHSA-N
SF4 (Subject of Investigation/LOI)	G [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
5AD (Subject of Investigation/LOI)	H [auth C]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N
MET (Subject of Investigation/LOI)	I [auth C]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Abbassi, N., Jaciuk, M., Lin, T.-Y., Glatt, S.

---

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101001394

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release