8J7R: J-K-St region of EMCV IRES

Name: PDB 8J7R: Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A (J-K-St/eIF4G focused)
Published: 2023-08-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A (J-K-St/eIF4G focused). Determined by electron microscopy at 3.7 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Encephalomyocarditis virus
Chains: 2
Atoms: 4,034
Mol. weight: 66.7 kDa
Ligands: MG
Released: 2 Aug 2023

Explore 8J7R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J7R contains 13 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	755-770	16
α-helix	776-784	9
α-helix	791-807	17
α-helix	809-811	3
α-helix	812-821	10
β-strand	827-828	2	1
β-strand	836-837	2	1
α-helix	839-851	13
α-helix	854-870	17
α-helix	874-907	34
α-helix	913-925	13
α-helix	929-946	18
α-helix	949-951	3
α-helix	952-968	17
α-helix	973-987	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4 gamma 1	B	protein	270	Homo sapiens	Q04637 (AlphaFold model)
Ires RNA (J-K-st)	C	RNA	108	Encephalomyocarditis virus

Sequence of entity 1 (B), FASTA

>8J7R_1 Eukaryotic translation initiation factor 4 gamma 1 (chains B)
MNHKVHHHHHHIEGRHMELGTLEDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQ
VTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKVPTTEKPTVTVNFRKL
LLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARDIARRRSLGNIKFI
GELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQM
EKIIKEKKTSSRIRFMLQDVLDLRGSNWVP

Sequence of entity 2 (C), FASTA

>8J7R_2 IRES RNA (J-K-St) (chains C)
GGGGCUGAAGGAUGCCCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGGGGCCUCGGUG
CACAUGCUUUACAUGUGUUUAGUCGAGGUUAAAAAACGUCUAGGCCCC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor. Imai, S., Suzuki, H., Fujiyoshi, Y. et al. Nat Commun (2023) 14:4977-4977. DOI 10.1038/s41467-023-40582-6 · PubMed

Other PDB entries of the same protein (UniProt Q04637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5T46 1.53 Å, Crystal structure of the human eIF4E-eIF4G complex
5EI3 1.71 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
4F02 2.0 Å, Crystal structure of the PABP-binding site of eIF4G in complex with RRM1-2 of PABP and…
4AZA 2.16 Å, Improved eIF4E binding peptides by phage display guided design.
1UG3 2.24 Å, C-terminal portion of human eIF4GI
5ZK5 2.25 Å, Stapled-peptides tailored against initiation of translation
2W97 2.29 Å, Crystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide
1LJ2 2.38 Å, Recognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization
5EHC 2.4 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
5EIR 2.69 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
8OZ0 3.5 Å, Structure of a human 48S translation initiation complex with eIF4F and eIF4A
6ZMW 3.7 Å, Structure of a human 48S translational initiation complex

Browse structure collections

About this viewer

MolViewer shows 8J7R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.