3EX7: EJC in its transition state

The crystal structure of EJC in its transition state. Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 10
Atoms: 11,856
Mol. weight: 197.21 kDa
Ligands: MG, AF3, ADP
Released: 9 Dec 2008

Explore 3EX7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EX7 contains 68 α-helices and 62 β-strands across 8 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	18-26	9	1
β-strand	31-37	7	1
α-helix	40-42	3
β-strand	46-52	7	1
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	81	1	2
β-strand	84	1	2
β-strand	85-92	8	1
β-strand	95-101	7	1
α-helix	107-111	5
α-helix	116-141	26
α-helix	142-144	3

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	1
β-strand	73-78	6	3
α-helix	86-94	9
β-strand	99-103	5	3
α-helix	105	1
β-strand	106	1	4
α-helix	107	1
β-strand	113	1	4
β-strand	117-121	5	3
α-helix	124-134	11
β-strand	138	1	5
β-strand	143	1	5
β-strand	145-148	4	3
β-strand	150-151	2	1

Chain C: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-56	10
α-helix	65-73	9
β-strand	78-81	4	6
α-helix	88-98	11
β-strand	109-112	4	6
α-helix	116-129	14
β-strand	137-140	4	6
α-helix	146-155	10
β-strand	159-162	4	6
α-helix	164-172	9
β-strand	183-187	5	6
α-helix	189-192	4
α-helix	198-205	8
β-strand	213-218	6	6
α-helix	223-226	4
α-helix	228-231	4
β-strand	237-239	3	6
α-helix	243-245	3
β-strand	251-257	7	7
α-helix	263-275	13
β-strand	279-283	5	7
α-helix	287-299	13
β-strand	305-307	3	7
α-helix	313-325	13
β-strand	330-333	4	7
α-helix	335-337	3
β-strand	346-351	6	7
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-381	7	7
α-helix	386-396	11
β-strand	400-402	3	7
α-helix	403-404	2
α-helix	407-411	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	233-240	8

Chain E: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	8
β-strand	18-26	9	8
β-strand	31-37	7	8
α-helix	40-42	3
β-strand	46-52	7	8
α-helix	54-67	14
α-helix	69-71	3
α-helix	74-76	3
β-strand	85-92	8	8
β-strand	95-101	7	8
α-helix	107-111	5
α-helix	116-141	26
α-helix	142-144	3

Chain G: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	8
β-strand	73-78	6	9
α-helix	86-94	9
β-strand	99-103	5	9
α-helix	105	1
β-strand	106	1	10
α-helix	107	1
β-strand	113	1	10
β-strand	116-121	6	9
α-helix	124-134	11
β-strand	138	1	11
β-strand	143	1	11
β-strand	145-148	4	9
β-strand	150-151	2	8

Chain H: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-55	9
α-helix	63-74	12
β-strand	78-80	3	12
α-helix	88-98	11
β-strand	109-112	4	12
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	12
α-helix	146-155	10
β-strand	159-162	4	12
α-helix	164-172	9
β-strand	183-187	5	12
α-helix	189-192	4
α-helix	198-206	9
β-strand	213-217	5	12
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	12
β-strand	251-257	7	13
α-helix	263-270	8
α-helix	272-275	4
β-strand	280-283	4	13
α-helix	287-299	13
β-strand	305-307	3	13
α-helix	313-324	12
β-strand	330-333	4	13
β-strand	348-351	4	13
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-381	7	13
α-helix	386-396	11
β-strand	400-402	3	13
α-helix	407-411	5

Chain I: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	172-174	3
α-helix	226-228	3
α-helix	230-232	3
α-helix	233-240	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein mago nashi homolog	A, E	protein	146	Homo sapiens	P61326 (AlphaFold model)
RNA-binding protein 8A	B, G	protein	126	Homo sapiens	Q9Y5S9 (AlphaFold model)
Eukaryotic initiation factor 4A-III	C, H	protein	413	Homo sapiens	P38919 (AlphaFold model)
Protein CASC3	D, I	protein	146	Homo sapiens	O15234 (AlphaFold model)
RNA (5'-r(upupupupupu)-3')	F, J	RNA	6

Sequence of entity 1 (A, E), FASTA

>3EX7_1 Protein mago nashi homolog (chains A, E)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 2 (B, G), FASTA

>3EX7_2 RNA-binding protein 8A (chains B, G)
REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT
GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPD
RRRRLE

Sequence of entity 3 (C, H), FASTA

>3EX7_3 Eukaryotic initiation factor 4A-III (chains C, H)
MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK
PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV
QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA
IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL
VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA
NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL
YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE

Sequence of entity 4 (D, I), FASTA

>3EX7_4 Protein CASC3 (chains D, I)
TKSTVTGERQSGDGQESTEPVENKVGKKGPKHLDDDEDRKNPAYIPRKGLFFEHDLRGQT
QEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHNPDDIKPRR
IRKPRYGSPPQRDPNWNGERLNKSHR

Sequence of entity 5 (F, J), FASTA

>3EX7_5 RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') (chains F, J)
UUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AF3	Aluminum fluoride	Al F3	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Mechanism of ATP turnover inhibition in the EJC. Nielsen, K.H., Chamieh, H., Andersen, C.B. et al. RNA (2009) 15:67-75. DOI 10.1261/rna.1283109 · PubMed

Other PDB entries of the same protein (UniProt P61326 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1P27 2.0 Å, Crystal Structure of the Human Y14/Magoh 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
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)
9XU3 3.0 Å, Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
2J0Q 3.2 Å, The crystal structure of the Exon Junction Complex at 3.2 A resolution
9FMD 3.3 Å, Integrative model of the human post-catalytic spliceosome (P-complex)
2XB2 3.4 Å, Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the…
8I0W 3.4 Å, The cryo-EM structure of human C complex
7W59 3.6 Å, The cryo-EM structure of human pre-C*-I complex

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