2HYI: Protein mago nashi homolog

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA. Determined by X-ray diffraction at 2.3 Å resolution. Released 15 Aug 2006.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,033
Mol. weight: 172.98 kDa
Ligands: MG, ANP
Released: 15 Aug 2006

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

Secondary structure: helices and β-sheets

2HYI contains 72 α-helices and 60 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, 6 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	85-92	8	1
β-strand	95-101	7	1
α-helix	107-112	6
α-helix	116-141	26
α-helix	142-144	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	1
β-strand	73-78	6	2
α-helix	86-93	8
α-helix	94-96	3
β-strand	99-106	8	2
α-helix	107	1
β-strand	113-121	9	2
α-helix	124-134	11
β-strand	138	1	3
β-strand	143	1	3
β-strand	145-148	4	2
β-strand	150-151	2	1

Chain C: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-56	10
α-helix	63-74	12
β-strand	78-81	4	4
α-helix	88-98	11
β-strand	109-112	4	4
α-helix	116-129	14
β-strand	137-140	4	4
α-helix	146-155	10
β-strand	159-162	4	4
α-helix	164-172	9
β-strand	183-187	5	4
α-helix	189-192	4
α-helix	198-205	8
β-strand	213-218	6	4
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	4
α-helix	243-245	3
β-strand	251-258	8	5
α-helix	262-272	11
α-helix	273-275	3
β-strand	279-283	5	5
α-helix	287-298	12
β-strand	305-307	3	5
α-helix	313-325	13
β-strand	330-333	4	5
α-helix	335-337	3
β-strand	346-351	6	5
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-382	8	5
α-helix	383-385	3
α-helix	386-396	11
β-strand	400-402	3	5
α-helix	408-412	5

Chain D: 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

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	6
β-strand	18-26	9	6
β-strand	31-37	7	6
α-helix	40-42	3
β-strand	46-52	7	6
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	81	1	7
β-strand	84	1	7
β-strand	85-92	8	6
β-strand	95-101	7	6
α-helix	107-110	4
α-helix	116-141	26
α-helix	142-144	3

Chain H: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	6
β-strand	73-78	6	8
α-helix	86-93	8
α-helix	94-96	3
β-strand	99-103	5	8
α-helix	105	1
β-strand	106	1	9
α-helix	107	1
β-strand	113	1	9
β-strand	117-121	5	8
α-helix	124-134	11
β-strand	138	1	10
β-strand	143	1	10
β-strand	145-148	4	8
β-strand	150-151	2	6

Chain I: 20 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	11
α-helix	88-98	11
β-strand	109-112	4	11
α-helix	116-129	14
β-strand	137-140	4	11
α-helix	146-155	10
β-strand	159-162	4	11
α-helix	164-172	9
β-strand	183-187	5	11
α-helix	189-192	4
α-helix	198-205	8
β-strand	213-218	6	11
α-helix	223-227	5
α-helix	229-231	3
β-strand	237-239	3	11
α-helix	243-245	3
β-strand	251-258	8	12
α-helix	262-275	14
β-strand	280-283	4	12
α-helix	287-299	13
β-strand	305-307	3	12
α-helix	313-325	13
β-strand	330-333	4	12
α-helix	335-337	3
β-strand	348-351	4	12
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-382	8	12
α-helix	385-395	11
β-strand	400-402	3	12
α-helix	407-412	6

Chain J: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	225-227	3
α-helix	230-232	3
α-helix	233-240	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-r(upupupupupu)-3'	F, L	RNA	6
Protein mago nashi homolog	A, G	protein	146	Homo sapiens	P61326 (AlphaFold model)
RNA-binding protein 8A	B, H	protein	91	Homo sapiens	Q9Y5S9 (AlphaFold model)
Probable ATP-dependent RNA helicase DDX48	C, I	protein	413	Homo sapiens	P38919 (AlphaFold model)
Protein CASC3	D, J	protein	77	Homo sapiens	O15234 (AlphaFold model)

Sequence of entity 1 (F, L), FASTA

>2HYI_1 5'-R(*UP*UP*UP*UP*UP*U)-3' (chains F, L)
UUUUUU

Sequence of entity 2 (A, G), FASTA

>2HYI_2 Protein mago nashi homolog (chains A, G)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 3 (B, H), FASTA

>2HYI_3 RNA-binding protein 8A (chains B, H)
PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET
YKEAQAAMEGLNGQDLMGQPISVDWCFVRGP

Sequence of entity 4 (C, I), FASTA

>2HYI_4 Probable ATP-dependent RNA helicase DDX48 (chains C, I)
MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK
PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV
QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA
IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL
VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA
NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL
YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE

Sequence of entity 5 (D, J), FASTA

>2HYI_5 Protein CASC3 (chains D, J)
LDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQA
PKSRQELIALYGYDIRS

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

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Andersen, C.B.F., 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 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
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)
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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