7ZNJ: ALYREF-exon junction complex hexamer

Structure of an ALYREF-exon junction complex hexamer. Determined by electron microscopy at 2.4 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 30
Atoms: 35,088
Mol. weight: 787.81 kDa
Ligands: ANP, MG
Released: 12 Apr 2023

Explore 7ZNJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZNJ contains 204 α-helices and 240 β-strands across 24 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	40-42	3
α-helix	47-56	10
α-helix	65-73	9
β-strand	78-81	4	21
α-helix	88-98	11
β-strand	109-112	4	21
α-helix	116-129	14
β-strand	137-140	4	21
α-helix	146-155	10
β-strand	159-162	4	21
α-helix	164-172	9
β-strand	183-187	5	21
α-helix	189-192	4
α-helix	198-206	9
α-helix	209	1
β-strand	213-218	6	21
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	21
α-helix	243-245	3
β-strand	251-257	7	22
α-helix	261-263	3
α-helix	264-270	7
α-helix	272-275	4
β-strand	279-283	5	22
α-helix	287-299	13
β-strand	305-307	3	22
α-helix	313-325	13
β-strand	330-333	4	22
α-helix	335-337	3
β-strand	346-351	6	22
α-helix	358-365	8
β-strand	375-381	7	22
α-helix	386-396	11
β-strand	401-402	2	22
α-helix	403	1

Chain A: 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	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	198-206	9
α-helix	209	1
β-strand	213-218	6	1
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	1
β-strand	251-257	7	2
α-helix	261-263	3
α-helix	264-270	7
α-helix	272-275	4
β-strand	279-283	5	2
α-helix	287-299	13
β-strand	306-307	2	2
α-helix	313-324	12
β-strand	330-333	4	2
β-strand	346-351	6	2
α-helix	358-365	8
β-strand	375-381	7	2
α-helix	386-395	10
β-strand	401-402	2	2
α-helix	403	1

Chains b, B, G and l: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	23
β-strand	18-26	9	23
β-strand	31-37	7	23
β-strand	46-51	6	23
β-strand	52	1	24
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	85-92	8	23
β-strand	95-102	8	23
α-helix	107-111	5
α-helix	116-141	26
α-helix	142-144	3

Chains c, C, h, H, m and M: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	25
β-strand	69	1	26
β-strand	72	1	26
β-strand	73-78	6	27
α-helix	86-93	8
β-strand	99-103	5	27
α-helix	105	1
β-strand	106	1	28
α-helix	107	1
β-strand	113	1	28
β-strand	116-121	6	27
α-helix	124-134	11
β-strand	138-139	2	29
β-strand	142-143	2	29
β-strand	145-148	4	27
β-strand	150	1	24
β-strand	151	1	25

Chains d, D, i, I, n and N: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	106-111	6	30
α-helix	119-126	8
β-strand	132-139	8	30
β-strand	145-153	9	30
α-helix	156-166	11
β-strand	170-171	2	31
β-strand	174-175	2	31
α-helix	176	1
β-strand	177-180	4	30

Chain f: 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	43
α-helix	88-98	11
β-strand	109-112	4	43
α-helix	116-129	14
β-strand	137-140	4	43
α-helix	146-155	10
β-strand	159-162	4	43
α-helix	164-172	9
β-strand	183-187	5	43
α-helix	189-192	4
α-helix	198-206	9
α-helix	209	1
β-strand	213-218	6	43
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	43
β-strand	251-257	7	44
α-helix	261-263	3
α-helix	264-270	7
α-helix	272-276	5
β-strand	279-283	5	44
α-helix	287-299	13
β-strand	305-307	3	44
α-helix	313-324	12
β-strand	330-333	4	44
α-helix	335-337	3
β-strand	346-351	6	44
α-helix	358-365	8
β-strand	375-381	7	44
α-helix	386-396	11
β-strand	401-402	2	44
α-helix	403	1

Chain F: 22 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	32
α-helix	88-98	11
β-strand	109-112	4	32
α-helix	116-129	14
β-strand	137-140	4	32
α-helix	146-155	10
β-strand	159-162	4	32
α-helix	164-172	9
β-strand	183-187	5	32
α-helix	189-192	4
α-helix	198-206	9
α-helix	209	1
β-strand	213-218	6	32
α-helix	223-228	6
α-helix	229-231	3
β-strand	237-239	3	32
α-helix	243-245	3
β-strand	251-257	7	33
α-helix	261-263	3
α-helix	264-270	7
α-helix	272-275	4
β-strand	279-283	5	33
α-helix	287-299	13
β-strand	305-307	3	33
α-helix	313-324	12
β-strand	330-333	4	33
α-helix	335-337	3
β-strand	346-351	6	33
α-helix	358-365	8
β-strand	375-381	7	33
α-helix	386-396	11
β-strand	401-402	2	33
α-helix	403	1

Chains g and L: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	45
β-strand	18-26	9	45
β-strand	31-37	7	45
β-strand	46-51	6	45
β-strand	52	1	46
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	85-92	8	45
β-strand	95-101	7	45
α-helix	107-111	5
α-helix	116-141	26
α-helix	142-144	3

2 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, N-terminally processed	A, F, K, a, f, k	protein	382	Homo sapiens	P38919 (AlphaFold model)
Protein mago nashi homolog	B, G, L, b, g, l	protein	146	Homo sapiens	P61326 (AlphaFold model)
RNA-binding protein 8A	C, H, M, c, h, m	protein	91	Homo sapiens	Q9Y5S9 (AlphaFold model)
Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4	D, I, N, d, i, n	protein	527	Homo sapiens	P0AEY0 (AlphaFold model), Q86V81
RNA	E, J, O, e, j, o	RNA	6	Homo sapiens

Sequence of entity 1 (A, F, K, a, f, k), FASTA

>7ZNJ_1 Eukaryotic initiation factor 4A-III, N-terminally processed (chains A, F, K, a, f, k)
MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS
QSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG
GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIY
DVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREE
WKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKE
FRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVK
NDDIRILRDIEQYYSTQIDEMP

Sequence of entity 2 (B, G, L, b, g, l), FASTA

>7ZNJ_2 Protein mago nashi homolog (chains B, G, L, b, g, l)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 3 (C, H, M, c, h, m), FASTA

>7ZNJ_3 RNA-binding protein 8A (chains C, H, M, c, h, m)
GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY
KEAQAAMEGLNGQDLMGQPISVDWCFVRGPP

Sequence of entity 4 (D, I, N, d, i, n), FASTA

>7ZNJ_4 Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4 (chains D, I, N, d, i, n)
MQLSHHHHHHHHHHSSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDK
LEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGK
LIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIA
ADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGET
AMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLEN
YLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYA
VRTAVINAASGRQTVDEALKDAQTSSGLEVLFQGPGSSGIRNRPAIARGAAGGGGRNRPA
PYSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA
AVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT

Sequence of entity 5 (E, J, O, e, j, o), FASTA

>7ZNJ_5 RNA (chains E, J, O, e, j, o)
UUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	6
MG	Magnesium ion	Mg	6

Primary citation

mRNA recognition and packaging by the human transcription-export complex. Pacheco-Fiallos, B., Vorlander, M.K., Riabov-Bassat, D. et al. Nature (2023) 616:828-835. DOI 10.1038/s41586-023-05904-0 · 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
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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