2XB2: Eukaryotic initiation factor 4A-III

Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery. Determined by X-ray diffraction at 3.4 Å resolution. Released 12 May 2010.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 13
Atoms: 11,710
Mol. weight: 208.45 kDa
Ligands: MG, ANP
Released: 12 May 2010

Explore 2XB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XB2 contains 70 α-helices and 66 β-strands across 10 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-72	10
β-strand	78-81	4	1
α-helix	88-98	11
β-strand	109-112	4	1
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	1
α-helix	146-155	10
β-strand	159-162	4	1
α-helix	164-172	9
β-strand	183-187	5	1
α-helix	189-192	4
α-helix	198-205	8
α-helix	209	1
β-strand	213-218	6	1
α-helix	223-228	6
β-strand	237-239	3	1
β-strand	251-258	8	2
α-helix	261-275	15
β-strand	280-283	4	2
α-helix	287-299	13
β-strand	305-307	3	2
α-helix	313-325	13
β-strand	330-333	4	2
α-helix	335-337	3
β-strand	348-351	4	2
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-382	8	2
α-helix	383-385	3
α-helix	386-395	10
β-strand	401-402	2	2
β-strand	404	1	3
α-helix	407-410	4

Chain C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-16	11	4
β-strand	18-26	9	4
β-strand	31-37	7	4
α-helix	40-42	3
β-strand	46-52	7	4
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	85-92	8	4
β-strand	95-101	7	4
α-helix	107-111	5
α-helix	116-141	26
α-helix	142-144	3

Chains D and Z: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	69	1	5
β-strand	72	1	5
β-strand	73-78	6	6
α-helix	86-94	9
β-strand	99-103	5	6
β-strand	106	1	7
β-strand	113	1	7
β-strand	116-121	6	6
α-helix	124-134	11
β-strand	138-139	2	8
β-strand	142-143	2	8
α-helix	144	1
β-strand	145-148	4	6
β-strand	150-151	2	4

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	424-427	4
β-strand	428	1	3

Chain S: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	230-232	3
α-helix	233-239	7

Chain T: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	226-228	3
α-helix	233-239	7

Chain U: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	424-426	3
β-strand	428	1	9

Chain X: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	41-43	3
α-helix	47-55	9
α-helix	63-72	10
β-strand	78-81	4	10
α-helix	88-98	11
β-strand	109-112	4	10
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	10
α-helix	146-155	10
β-strand	159-162	4	10
α-helix	164-172	9
β-strand	183-187	5	10
α-helix	189-192	4
α-helix	198-205	8
α-helix	209	1
β-strand	213-218	6	10
α-helix	223-227	5
α-helix	228-230	3
β-strand	237-239	3	10
β-strand	251-258	8	11
α-helix	261-275	15
β-strand	280-283	4	11
α-helix	287-299	13
β-strand	305-307	3	11
α-helix	313-325	13
β-strand	330-333	4	11
α-helix	335-337	3
β-strand	348-351	4	11
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-382	8	11
α-helix	383-385	3
α-helix	386-395	10
β-strand	401-402	2	11
β-strand	404	1	9
α-helix	407-410	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic initiation factor 4A-III	A, X	protein	411	HOMO SAPIENS	P38919 (AlphaFold model)
Protein mago nashi homolog	C, Y	protein	146	HOMO SAPIENS	P61326 (AlphaFold model)
RNA-binding protein 8A	D, Z	protein	90	HOMO SAPIENS	Q9Y5S9 (AlphaFold model)
RNA poly-U-ribonucleotide	E, R	RNA	15	SYNTHETIC CONSTRUCT
Putative regulator of nonsense transcripts 3B	F	protein	3	HOMO SAPIENS	Q9BZI7 (AlphaFold model)
Regulator of nonsense transcripts 3B	G, U	protein	60	HOMO SAPIENS	Q9BZI7 (AlphaFold model)
Protein CASC3	S, T	protein	150	HOMO SAPIENS	O15234

Sequence of entity 1 (A, X), FASTA

>2XB2_1 EUKARYOTIC INITIATION FACTOR 4A-III (chains A, X)
MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK
PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV
QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA
IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL
VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA
NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL
YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Sequence of entity 2 (C, Y), FASTA

>2XB2_2 PROTEIN MAGO NASHI HOMOLOG (chains C, Y)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 3 (D, Z), FASTA

>2XB2_3 RNA-BINDING PROTEIN 8A (chains D, Z)
PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK
EAQAAMEGLNGQDLMGQPISVDWCFVRGPP

Sequence of entity 4 (E, R), FASTA

>2XB2_4 RNA POLY-U-RIBONUCLEOTIDE (chains E, R)
UUUUUUUUUUUUUUU

Sequence of entity 5 (F), FASTA

>2XB2_5 PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B (chains F)
AER

Sequence of entity 6 (G, U), FASTA

>2XB2_6 REGULATOR OF NONSENSE TRANSCRIPTS 3B (chains G, U)
EVVKRDRIRNKDRPAMQLYQPGARSRNRLCPPDDSTKSGDSAAERKQESGISHRKEGGEE

Sequence of entity 7 (S, T), FASTA

>2XB2_7 PROTEIN CASC3 (chains S, T)
DTKSTVTGERQSGDGQESTEPVENKVGKKGPKHLDDDEDRKNPAYIPRKGLFFEHDLRGQ
TQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHNPDDIKPR
RIRKPRYGSPPQRDPNWNGERLNKSHRHQG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Insights Into the Recruitment of the Nmd Machinery from the Crystal Structure of a Core Ejc-Upf3B Complex. Buchwald, G., Ebert, J., Basquin, C. et al. Proc Natl Acad Sci U S A (2010) 107:10050. DOI 10.1073/PNAS.1000993107 · 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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