2HXY: Human apo-eIF4AIII

Crystal structure of human apo-eIF4AIII. Determined by X-ray diffraction at 3.3 Å resolution. Released 15 Aug 2006.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,080
Mol. weight: 179.27 kDa
Released: 15 Aug 2006

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

Secondary structure: helices and β-sheets

2HXY contains 78 α-helices and 64 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: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-74	12
β-strand	78-81	4	1
α-helix	82	1
α-helix	90-98	9
β-strand	109-112	4	1
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	1
α-helix	146-156	11
β-strand	159-162	4	1
α-helix	164-172	9
β-strand	183-186	4	1
α-helix	189-194	6
α-helix	198-207	10
β-strand	213-218	6	1
α-helix	225-229	5
β-strand	237-239	3	1
β-strand	247	1	2
β-strand	251-255	5	3
α-helix	262-275	14
β-strand	280-282	3	3
α-helix	287-298	12
β-strand	304-307	4	3
α-helix	316-325	10
β-strand	330-333	4	3
β-strand	348-351	4	3
α-helix	361-365	5
β-strand	367	1	2
β-strand	375-379	5	3
α-helix	383-395	13
β-strand	401-402	2	3
α-helix	403-404	2

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-74	12
β-strand	78-81	4	4
α-helix	82	1
α-helix	90-98	9
β-strand	109-112	4	4
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	4
α-helix	146-156	11
β-strand	159-162	4	4
α-helix	164-172	9
β-strand	183-186	4	4
α-helix	189-194	6
α-helix	198-207	10
β-strand	213-218	6	4
α-helix	225-229	5
β-strand	237-239	3	4
β-strand	247	1	5
β-strand	252-257	6	6
α-helix	262-272	11
β-strand	280-284	5	6
α-helix	287-298	12
β-strand	304-307	4	6
α-helix	313-325	13
β-strand	330-334	5	6
β-strand	348-351	4	6
α-helix	358-365	8
β-strand	367	1	5
α-helix	373-374	2
β-strand	376-381	6	6
α-helix	383-395	13
β-strand	401-402	2	6
α-helix	403-404	2

Chain C: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-74	12
β-strand	78-81	4	7
α-helix	82	1
α-helix	90-98	9
β-strand	109-112	4	7
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	7
α-helix	146-156	11
β-strand	159-162	4	7
α-helix	164-172	9
β-strand	183-186	4	7
α-helix	189-194	6
α-helix	198-205	8
β-strand	213-218	6	7
α-helix	225-229	5
β-strand	237-239	3	7
β-strand	247	1	8
β-strand	252-255	4	9
α-helix	262-271	10
α-helix	273-276	4
β-strand	281-284	4	9
α-helix	287-298	12
β-strand	305-307	3	9
α-helix	313-325	13
β-strand	331-334	4	9
β-strand	348-351	4	9
α-helix	361-365	5
β-strand	367	1	8
α-helix	372-374	3
β-strand	376-379	4	9
α-helix	383-385	3
α-helix	386-396	11
β-strand	401-402	2	9
α-helix	407-411	5

Chain D: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-74	12
β-strand	78-81	4	10
α-helix	82	1
α-helix	90-98	9
β-strand	109-112	4	10
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	10
α-helix	146-156	11
β-strand	159-162	4	10
α-helix	164-172	9
β-strand	183-186	4	10
α-helix	189-194	6
α-helix	198-207	10
α-helix	209	1
β-strand	213-218	6	10
α-helix	225-229	5
β-strand	237-239	3	10
β-strand	247	1	11
β-strand	252-256	5	12
α-helix	262-272	11
β-strand	281-284	4	12
α-helix	287-298	12
β-strand	304-307	4	12
α-helix	313-325	13
β-strand	330-334	5	12
β-strand	348-351	4	12
α-helix	359-365	7
β-strand	367	1	11
β-strand	376-380	5	12
α-helix	383-385	3
α-helix	388-396	9
β-strand	401-402	2	12
α-helix	403-404	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX48	A, B, C, D	protein	391	Homo sapiens	P38919 (AlphaFold model)

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

>2HXY_1 Probable ATP-dependent RNA helicase DDX48 (chains A, B, C, D)
MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS
QSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG
GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIY
DVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREE
WKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKE
FRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVK
NDDIRILRDIEQYYSTQIDEMPMNVADLILE

Primary citation

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Andersen, C.B., Ballut, L., Johansen, J.S. et al. Science (2006) 313:1968-1972. DOI 10.1126/science.1131981 · PubMed

Other PDB entries of the same protein (UniProt P38919 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C9B 2.0 Å, Crystal structure of eIF4AIII-CWC22 complex
2J0S 2.21 Å, The crystal structure of the Exon Junction Complex at 2.2 A resolution
2HYI 2.3 Å, Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA
3EX7 2.3 Å, The crystal structure of EJC in its transition state
7ZNJ 2.4 Å, Structure of an ALYREF-exon junction complex hexamer
8C6J 2.8 Å, Human spliceosomal PM5 C* complex
9XTT 2.92 Å, Human minor spliceosome branching-completed C complex (after step-I)
2J0U 3.0 Å, The crystal structure of eIF4AIII-Barentsz complex at 3.0 A resolution
6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
9XU3 3.0 Å, Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
6YVH 3.19 Å, CWC22-CWC27-EIF4A3 Complex
2J0Q 3.2 Å, The crystal structure of the Exon Junction Complex at 3.2 A resolution

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