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

Name: PDB 8HUJ: Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A
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. Determined by electron microscopy at 3.76 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 3.76 Å
Organisms: Homo sapiens, Encephalomyocarditis virus
Chains: 3
Atoms: 7,143
Mol. weight: 115.36 kDa
Ligands: MG
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

8HUJ contains 34 α-helices and 17 β-strands across 2 chains. 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 A: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
α-helix	35-37	3
α-helix	41-50	10
α-helix	57-61	5
α-helix	64-68	5
β-strand	72-75	4	1
α-helix	82-93	12
β-strand	103-106	4	1
α-helix	111-122	12
β-strand	131-133	3	1
α-helix	140-149	10
β-strand	154-156	3	1
α-helix	159-166	8
β-strand	178-182	5	1
α-helix	184-190	7
α-helix	193-202	10
β-strand	208-213	6	1
α-helix	218-227	10
β-strand	232-235	4	1
α-helix	243-245	3
β-strand	247-251	5	2
α-helix	258-268	11
β-strand	275-278	4	2
α-helix	283-294	12
β-strand	300-301	2	2
α-helix	309-320	12
β-strand	325-328	4	2
α-helix	330-335	6
β-strand	343-346	4	2
α-helix	355-360	6
α-helix	362-364	3
β-strand	371-375	5	2
α-helix	378-380	3
α-helix	381-390	10
β-strand	396-397	2	2
α-helix	402-405	4

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	3
β-strand	836-837	2	3
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 initiation factor 4A-I	A	protein	428	Homo sapiens	P60842 (AlphaFold model)
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 (A), FASTA

>8HUJ_1 Eukaryotic initiation factor 4A-I (chains A)
MGSSHHHHHHHHSSGLEVLFQGPSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMN
LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL
KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT
PGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPS
DVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF
INTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDV
QQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEM
PLNVADLI

Sequence of entity 2 (B), FASTA

>8HUJ_2 Eukaryotic translation initiation factor 4 gamma 1 (chains B)
MNHKVHHHHHHIEGRHMELGTLEDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQ
VTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKVPTTEKPTVTVNFRKL
LLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARDIARRRSLGNIKFI
GELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQM
EKIIKEKKTSSRIRFMLQDVLDLRGSNWVP

Sequence of entity 3 (C), FASTA

>8HUJ_3 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 P60842 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ZBZ 1.31 Å, Crystal structure of the DEAD domain of Human eIF4A with sanguinarine
9DTS 1.69 Å, Crystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/polypurine RNA complex
9I9G 1.7 Å, Crystal structure of human eIF4A1 C-terminal domain in complex with hippuristanol
9AVR 1.91 Å, Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol
5ZC9 2.0 Å, Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex
2G9N 2.25 Å, Structure of the DEAD domain of Human eukaryotic initiation factor 4A, eIF4A
7PPZ 2.52 Å, Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in…
9I9F 2.73 Å, Crystal structure of apoform human eIF4A1 C-terminal domain
2ZU6 2.8 Å, crystal structure of the eIF4A-PDCD4 complex
7PQ0 3.0 Å, Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in…
3EIQ 3.5 Å, Crystal structure of Pdcd4-eIF4A
8OZ0 3.5 Å, Structure of a human 48S translation initiation complex with eIF4F and eIF4A

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