2J0S: Exon Junction Complex

The crystal structure of the Exon Junction Complex at 2.2 A resolution. Determined by X-ray diffraction at 2.21 Å resolution. Released 6 Sept 2006.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: HOMO SAPIENS
Chains: 5
Atoms: 5,906
Mol. weight: 97 kDa
Ligands: ANP, MG
Released: 6 Sept 2006

Explore 2J0S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2J0S contains 34 α-helices and 29 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: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	47-56	10
α-helix	63-73	11
β-strand	78-81	4	1
α-helix	88-98	11
β-strand	109-112	4	1
α-helix	116-129	14
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	223-226	4
α-helix	229-231	3
β-strand	237-239	3	1
α-helix	243-245	3
β-strand	251-258	8	2
α-helix	263-275	13
β-strand	279-283	5	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	346-351	6	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
α-helix	403-404	2

Chain C: 7 helices, 6 β-strands

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

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	69	1	4
β-strand	72	1	4
β-strand	73-78	6	5
α-helix	86-94	9
β-strand	99-106	8	5
α-helix	107	1
β-strand	113-121	9	5
α-helix	124-134	11
β-strand	138	1	6
β-strand	143	1	6
β-strand	145-148	4	5
β-strand	150-151	2	3

Chain T: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	172-174	3
α-helix	226-228	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase DDX48	A	protein	410	HOMO SAPIENS	P38919 (AlphaFold model)
Protein mago nashi homolog	C	protein	146	HOMO SAPIENS	P61326 (AlphaFold model)
RNA-binding protein 8A	D	protein	89	HOMO SAPIENS	Q9Y5S9 (AlphaFold model)
5'-r(upupupupupupupupupup upupupup*u)-3'	E	RNA	15
Protein CASC3	T	protein	150	HOMO SAPIENS	O15234 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2J0S_1 ATP-DEPENDENT RNA HELICASE DDX48 (chains A)
ATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKP
SAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQ
IQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAI
KMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV
KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREAN
FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY
IHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Sequence of entity 2 (C), FASTA

>2J0S_2 PROTEIN MAGO NASHI HOMOLOG (chains C)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 3 (D), FASTA

>2J0S_3 RNA-BINDING PROTEIN 8A (chains D)
PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK
EAQAAMEGLNGQDLMGQPISVDWCFVRGP

Sequence of entity 4 (E), FASTA

>2J0S_4 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP *UP*UP*UP*UP*U)-3' (chains E)
UUUUUUUUUUUUUUU

Sequence of entity 5 (T), FASTA

>2J0S_5 PROTEIN CASC3 (chains T)
DTKSTVTGERQSGDGQESTEPVENKVGKKGPKHLDDDEDRKNPAYIPRKGLFFEHDLRGQ
TQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHNPDDIKPR
RIRKPRYGSPPQRDPNWNGERLNKSHRHQG

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	1

Primary citation

The Crystal Structure of the Exon Junction Complex Reveals How It Mantains a Stable Grip on Mrna. Bono, F., Ebert, J., Lorentzen, E. et al. Cell (2006) 126:713. DOI 10.1016/J.CELL.2006.08.006 · 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
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
2HXY 3.3 Å, Crystal structure of human apo-eIF4AIII

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