9DTS: Eukaryotic initiation factor 4A-I

Crystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/polypurine RNA complex. Determined by X-ray diffraction at 1.69 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,029
Mol. weight: 194.6 kDa
Ligands: A1BB1, ANP, MG
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9DTS contains 86 α-helices and 56 β-strands across 4 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	41-50	10
α-helix	57-67	11
β-strand	72-75	4	1
α-helix	82-93	12
β-strand	103-106	4	1
α-helix	110-123	14
β-strand	131-134	4	1
α-helix	140-149	10
β-strand	154-157	4	1
α-helix	159-167	9
β-strand	178-182	5	1
α-helix	184-187	4
α-helix	190-200	11
β-strand	208-213	6	1
α-helix	218-224	7
β-strand	232-234	3	1
α-helix	238-240	3
β-strand	246-254	9	2
α-helix	256-258	3
α-helix	259-269	11
β-strand	274-278	5	2
α-helix	282-294	13
β-strand	300-302	3	2
α-helix	308-320	13
β-strand	325-328	4	2
α-helix	330-332	3
β-strand	341-346	6	2
α-helix	349-350	2
α-helix	353-360	8
α-helix	365-367	3
β-strand	370-377	8	2
α-helix	380-391	12
β-strand	396-397	2	2
α-helix	398-399	2

Chain B: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	41-50	10
α-helix	57-67	11
β-strand	72-75	4	3
α-helix	82-93	12
β-strand	103-106	4	3
α-helix	110-123	14
β-strand	131-134	4	3
α-helix	140-149	10
β-strand	154-157	4	3
α-helix	159-167	9
β-strand	178-181	4	3
α-helix	184-187	4
α-helix	193-200	8
β-strand	208-213	6	3
α-helix	218-223	6
α-helix	224-226	3
β-strand	232-234	3	3
α-helix	238-240	3
β-strand	246-254	9	4
α-helix	256-258	3
α-helix	259-269	11
β-strand	274-278	5	4
α-helix	282-294	13
β-strand	300-302	3	4
α-helix	308-320	13
β-strand	325-328	4	4
α-helix	330-332	3
β-strand	341-346	6	4
α-helix	349-350	2
α-helix	353-360	8
α-helix	365-367	3
β-strand	370-377	8	4
α-helix	381-390	10
β-strand	396-397	2	4

Chain C: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	41-50	10
α-helix	57-67	11
β-strand	72-75	4	5
α-helix	82-93	12
β-strand	103-106	4	5
α-helix	110-123	14
β-strand	131-134	4	5
α-helix	140-149	10
β-strand	154-157	4	5
α-helix	159-167	9
β-strand	178-182	5	5
α-helix	184-187	4
α-helix	190-200	11
β-strand	208-213	6	5
α-helix	218-224	7
β-strand	232-234	3	5
α-helix	238-240	3
β-strand	246-252	7	6
α-helix	256-258	3
α-helix	259-270	12
β-strand	274-278	5	6
α-helix	282-294	13
β-strand	300-302	3	6
α-helix	308-319	12
β-strand	325-328	4	6
α-helix	330-332	3
β-strand	341-346	6	6
α-helix	349-350	2
α-helix	353-360	8
α-helix	365-367	3
β-strand	370-376	7	6
α-helix	378-391	14
β-strand	396-397	2	6
α-helix	398	1
α-helix	402-404	3

Chain D: 22 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	7
α-helix	82-93	12
β-strand	103-106	4	7
α-helix	110-123	14
α-helix	125-127	3
β-strand	131-134	4	7
α-helix	140-149	10
β-strand	154-157	4	7
α-helix	159-167	9
β-strand	178-182	5	7
α-helix	184-187	4
α-helix	190-200	11
β-strand	208-213	6	7
α-helix	218-223	6
α-helix	224-226	3
β-strand	232-234	3	7
α-helix	238-240	3
β-strand	246-252	7	8
α-helix	259-270	12
β-strand	274-278	5	8
α-helix	282-294	13
β-strand	300-302	3	8
α-helix	308-320	13
β-strand	325-328	4	8
α-helix	330-332	3
β-strand	341-346	6	8
α-helix	349-350	2
α-helix	354-360	7
α-helix	361-363	3
β-strand	370-376	7	8
α-helix	381-391	11
β-strand	396-397	2	8
α-helix	398	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic initiation factor 4A-I	A, B, C, D	protein	388	Homo sapiens	P60842 (AlphaFold model)
RNA (5'-r(papgpapgpapgpapg)-3')	W, X, Y, Z	RNA	10	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>9DTS_1 Eukaryotic initiation factor 4A-I (chains A, B, C, D)
SSGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQS
GTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT
NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYD
IFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEW
KLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF
RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE
EDKRTLRDIETFYNTSIEEMPLNVADLI

Sequence of entity 2 (W, X, Y, Z), FASTA

>9DTS_2 RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3') (chains W, X, Y, Z)
AGAGAGAGAG

Ligands and cofactors

ID	Name	Formula	Copies
A1BB1	(3aR,4R,5S,5aR,10bR)-3a-hydroxy-N,8,10-trimethoxy-5a-(4-methoxyphenyl)-N,2-dime…	C31 H33 N3 O7	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	4
MG	Magnesium ion	Mg	4

Primary citation

Structural Basis for the Improved RNA Clamping of Amidino-Rocaglates to eIF4A1. Conley, J.F., Brown, L.E., McNeely, J.H. et al. ACS Omega (2025) 10:5795-5808. DOI 10.1021/acsomega.4c09421 · 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
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
8XXN 3.6 Å, Cryo-EM structure of the human 43S ribosome with PDCD4

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