2ZU6: EIF4A-PDCD4 complex

crystal structure of the eIF4A-PDCD4 complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Feb 2009.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,986
Mol. weight: 246.92 kDa
Released: 24 Feb 2009

Explore 2ZU6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZU6 contains 94 α-helices and 62 β-strands across 6 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: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	1
β-strand	72-75	4	1
α-helix	84-91	8
β-strand	103-106	4	1
α-helix	110-127	18
β-strand	131-133	3	1
α-helix	140-150	11
β-strand	154-157	4	1
α-helix	159-166	8
β-strand	178-182	5	1
α-helix	184-189	6
α-helix	193-201	9
β-strand	208-213	6	1
α-helix	218-227	10
α-helix	231	1
β-strand	232-236	5	1
β-strand	241-242	2	2
β-strand	246-251	6	3
α-helix	256-269	14
β-strand	275-278	4	3
α-helix	282-290	9
β-strand	300-301	2	3
α-helix	312-316	5
α-helix	318-320	3
β-strand	325-328	4	3
α-helix	330-333	4
β-strand	343-346	4	3
α-helix	354-360	7
β-strand	362-363	2	2
β-strand	370-375	6	3
α-helix	378-391	14
β-strand	396-397	2	3
α-helix	398	1

Chain B: 17 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	164-178	15
α-helix	181-189	9
α-helix	194-199	6
α-helix	200-209	10
α-helix	213-229	17
β-strand	231	1	4
α-helix	233-253	21
α-helix	257-270	14
α-helix	280-282	3
α-helix	289-303	15
α-helix	324-341	18
α-helix	344-354	11
α-helix	357-359	3
α-helix	360-372	13
α-helix	378-393	16
α-helix	398-418	21
α-helix	422-436	15
α-helix	441-445	5

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	41-48	8
α-helix	58-61	4
α-helix	65-68	4
β-strand	72-75	4	5
α-helix	82-92	11
β-strand	103-106	4	5
α-helix	110-121	12
β-strand	132-133	2	5
α-helix	141-149	9
β-strand	155-157	3	5
α-helix	159-167	9
β-strand	178-181	4	5
α-helix	184-189	6
α-helix	193-200	8
β-strand	208-213	6	5
α-helix	218-227	10
β-strand	232-235	4	5
β-strand	247-252	6	6
α-helix	258-270	13
β-strand	276-278	3	6
α-helix	282-293	12
β-strand	300-302	3	6
α-helix	308-318	11
β-strand	326-328	3	6
α-helix	333-335	3
β-strand	343-346	4	6
α-helix	353-360	8
β-strand	371-376	6	6
α-helix	381-383	3
α-helix	387-390	4
β-strand	396-397	2	6

Chain D: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	7
β-strand	72-75	4	7
α-helix	84-91	8
β-strand	103-106	4	7
α-helix	110-122	13
β-strand	131-133	3	7
α-helix	140-150	11
β-strand	154-157	4	7
α-helix	159-167	9
β-strand	178-182	5	7
α-helix	184-189	6
α-helix	193-201	9
β-strand	208-213	6	7
α-helix	218-227	10
α-helix	231	1
β-strand	232-236	5	7
α-helix	239-240	2
β-strand	241-242	2	8
β-strand	246-251	6	9
α-helix	256-269	14
β-strand	276-278	3	9
α-helix	282-293	12
β-strand	300-301	2	9
β-strand	326-328	3	9
α-helix	330-334	5
β-strand	343-346	4	9
α-helix	355-360	6
β-strand	362-363	2	8
β-strand	370-375	6	9
α-helix	381-390	10
β-strand	396-397	2	9

Chain E: 19 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	164-178	15
α-helix	181-189	9
α-helix	196-198	3
α-helix	199-209	11
α-helix	213-229	17
β-strand	231	1	10
α-helix	233-253	21
α-helix	257-270	14
α-helix	278-281	4
α-helix	289-304	16
α-helix	324-341	18
α-helix	344-353	10
α-helix	357-359	3
α-helix	360-373	14
α-helix	378-393	16
α-helix	398-410	13
α-helix	412-418	7
α-helix	422-434	13
α-helix	441-444	4
α-helix	448-449	2

Chain F: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	103-106	4	11
α-helix	110-121	12
β-strand	133	1	11
α-helix	141-148	8
β-strand	155-157	3	11
α-helix	159-167	9
β-strand	178-181	4	11
α-helix	184-188	5
α-helix	193-200	8
β-strand	208	1	11
α-helix	218-227	10
β-strand	247-252	6	12
α-helix	258-266	9
β-strand	276-278	3	12
α-helix	282-293	12
β-strand	300-302	3	12
α-helix	315-318	4
β-strand	326-328	3	12
α-helix	331-333	3
β-strand	344-346	3	12
α-helix	353-359	7
β-strand	371-376	6	12
β-strand	396-397	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic initiation factor 4A-I	A, C, D, F	protein	388	Homo sapiens	P60842 (AlphaFold model)
Programmed cell death protein 4	B, E	protein	307	Homo sapiens	Q53EL6 (AlphaFold model)

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

>2ZU6_1 Eukaryotic initiation factor 4A-I (chains A, C, D, F)
MEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQS
GTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT
NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYD
IFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEW
KLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF
RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE
EDKRTLRDIETFYNTSIEEMPLNVADLI

Sequence of entity 2 (B, E), FASTA

>2ZU6_2 Programmed cell death protein 4 (chains B, E)
AFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKL
LSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSY
KGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSG
DISEAEHCLKELEVPHFHHELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMK
RGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRGRKRFVSEGDGG
RLKPESY

Primary citation

Crystal structure of the eIF4A-PDCD4 complex. Chang, J.H., Cho, Y.H., Sohn, S.Y. et al. Proc Natl Acad Sci U S A (2009) 106:3148-3153. DOI 10.1073/pnas.0808275106 · 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
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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