9AVR: Human eIF4A-1

Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol. Determined by X-ray diffraction at 1.91 Å resolution. Released 23 Oct 2024.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,561
Mol. weight: 50.97 kDa
Ligands: ANP, MG, A1AG8
Released: 23 Oct 2024

Explore 9AVR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AVR contains 20 α-helices and 14 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 A: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	41-50	10
α-helix	57-68	12
β-strand	72-75	4	1
α-helix	82-93	12
β-strand	103-106	4	1
α-helix	110-124	15
β-strand	131-134	4	1
α-helix	140-149	10
β-strand	154-157	4	1
α-helix	159-168	10
β-strand	178-182	5	1
α-helix	184-187	4
α-helix	193-200	8
β-strand	208-213	6	1
α-helix	218-227	10
β-strand	232-234	3	1
α-helix	238-240	3
β-strand	246-252	7	2
α-helix	253-254	2
α-helix	259-268	10
β-strand	274-278	5	2
α-helix	282-293	12
β-strand	300-302	3	2
α-helix	308-319	12
β-strand	325-328	4	2
α-helix	330-332	3
β-strand	341-346	6	2
α-helix	353-360	8
α-helix	365-367	3
β-strand	370-376	7	2
α-helix	378-380	3
α-helix	381-391	11
β-strand	395-397	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic initiation factor 4A-I	A	protein	406	Homo sapiens	P60842 (AlphaFold model)
RNA oligonucleotide (AG)5	B	RNA	10	Homo sapiens

Sequence of entity 1 (A), FASTA

>9AVR_1 Eukaryotic initiation factor 4A-I (chains A)
MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQ
RAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVV
MALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFV
LDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEE
LTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVS
AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRI
GRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI

Sequence of entity 2 (B), FASTA

>9AVR_2 RNA oligonucleotide (AG)5 (chains B)
AGAGAGAGAG

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	1
A1AG8	silvestrol	C34 H38 O13	1

Water and common crystallization additives (IOD) are not listed.

Primary citation

Protein-RNA interactions mediated by silvestrol-insight into a unique molecular clamp. Naineni, S.K., Bhatt, G., Jiramongkolsiri, E. et al. Nucleic Acids Res (2024) 52:12701-12711. DOI 10.1093/nar/gkae824 · 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
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
8XXN 3.6 Å, Cryo-EM structure of the human 43S ribosome with PDCD4

Browse structure collections

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