5ZC9: Eukaryotic initiation factor 4A-I

Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 3,558
Mol. weight: 49.26 kDa
Ligands: RCG, MG, ANP
Released: 16 Jan 2019

Explore 5ZC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZC9 contains 24 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: 24 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	178-181	4	1
α-helix	184-187	4
α-helix	193-200	8
β-strand	208-213	6	1
α-helix	218-223	6
α-helix	224-226	3
β-strand	232-234	3	1
α-helix	238-240	3
β-strand	246-254	9	2
α-helix	256-258	3
α-helix	259-265	7
α-helix	267-270	4
β-strand	274-278	5	2
α-helix	282-294	13
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	349-350	2
α-helix	353-360	8
α-helix	365-367	3
β-strand	370-377	8	2
α-helix	378-391	14
β-strand	396-397	2	2
α-helix	398-399	2
α-helix	400-404	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic initiation factor 4A-I	A	protein	394	Homo sapiens	P60842 (AlphaFold model)
RNA (5'-r(apgpapgpapgpapgpapg)-3')	B	RNA	10	synthetic construct

Sequence of entity 1 (A), FASTA

>5ZC9_1 Eukaryotic initiation factor 4A-I (chains A)
GPGYQDPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDV
IAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCH
ACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGF
KDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYIN
VEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERD
VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVA
INMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI

Sequence of entity 2 (B), FASTA

>5ZC9_2 RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3') (chains B)
AGAGAGAGAG

Ligands and cofactors

ID	Name	Formula	Copies
RCG	(1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxi…	C29 H31 N O7	1
MG	Magnesium ion	Mg	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Iwasaki, S., Iwasaki, W., Takahashi, M. et al. Mol Cell (2019) 73:738. DOI 10.1016/j.molcel.2018.11.026 · 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
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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