7ZNK: Endogenous human TREX complex

Structure of an endogenous human TREX complex bound to mRNA. Determined by electron microscopy at 3.9 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 32
Atoms: 88,261
Mol. weight: 2002.52 kDa
Released: 3 May 2023

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

Secondary structure: helices and β-sheets

7ZNK contains 480 α-helices and 350 β-strands across 30 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.

Chains a and A: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	11-21	11
α-helix	31-36	6
α-helix	45-64	20
α-helix	72-83	12
α-helix	92-103	12
α-helix	107-119	13
α-helix	134-146	13
α-helix	153-166	14
α-helix	232-246	15
α-helix	248-250	3
α-helix	254-274	21
α-helix	310-313	4
α-helix	315-333	19
α-helix	347-365	19
α-helix	371-388	18
α-helix	436-442	7
α-helix	490-502	13
α-helix	518-527	10

Chains b and B: 61 helices, 0 β-strands

Element	Residues	Length
α-helix	15-22	8
α-helix	40-56	17
α-helix	73-79	7
α-helix	84-99	16
α-helix	108-118	11
α-helix	143-155	13
α-helix	169-179	11
α-helix	189-203	15
α-helix	207-220	14
α-helix	225-236	12
α-helix	242-253	12
α-helix	264-275	12
α-helix	281-287	7
α-helix	294-307	14
α-helix	344-352	9
α-helix	359-366	8
α-helix	377-398	22
α-helix	400-401	2
α-helix	426	1
α-helix	427-431	5
α-helix	432-435	4
α-helix	442-444	3
α-helix	446-463	18
α-helix	474-486	13
α-helix	487-491	5
α-helix	492-495	4
α-helix	504-512	9
α-helix	517-529	13
α-helix	536-553	18
α-helix	565-574	10
α-helix	576-590	15
α-helix	594-600	7
α-helix	606-621	16
α-helix	637-652	16
α-helix	659-669	11
α-helix	676-685	10
α-helix	697-702	6
α-helix	708-712	5
α-helix	725-736	12
α-helix	739-755	17
α-helix	765-787	23
α-helix	790-796	7
α-helix	800-806	7
α-helix	811-822	12
α-helix	861-868	8
α-helix	878-886	9
α-helix	900-907	8
α-helix	929-961	33
α-helix	973-977	5
α-helix	978-982	5
α-helix	983-988	6
α-helix	990-998	9
α-helix	999-1004	6
α-helix	1005	1
α-helix	1013-1022	10
α-helix	1024-1029	6
α-helix	1035-1052	18
α-helix	1091-1112	22
α-helix	1117-1129	13
α-helix	1138-1153	16
α-helix	1161-1175	15

Chains c, C, k and K: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
β-strand	47-54	8	69
β-strand	58-63	6	70
β-strand	69-74	6	70
β-strand	78-84	7	70
β-strand	89-96	8	70
β-strand	102-107	6	71
β-strand	114-119	6	71
β-strand	123-128	6	71
β-strand	133-139	7	71
β-strand	144-149	6	72
β-strand	155-160	6	72
β-strand	164-169	6	72
β-strand	175-180	6	72
β-strand	185-190	6	73
β-strand	196-201	6	73
β-strand	205-210	6	73
β-strand	215-221	7	73
β-strand	227-232	6	74
β-strand	238-243	6	74
β-strand	248-252	5	74
β-strand	257-262	6	74
β-strand	269-274	6	75
β-strand	280-285	6	75
β-strand	290-294	5	75
β-strand	303-304	2	75
β-strand	312-314	3	69
β-strand	322-325	4	69
β-strand	340-346	7	69

Chains e and E: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	39-46	8
α-helix	53-74	22
α-helix	81-143	63
α-helix	190-246	57
α-helix	253-261	9
α-helix	266-281	16
β-strand	286-291	6	76
α-helix	294-298	5
α-helix	334-340	7
β-strand	343	1	76
β-strand	347-354	8	76
β-strand	358-367	10	76
β-strand	372-381	10	76
α-helix	416-423	8
α-helix	431-437	7
β-strand	439	1	76
α-helix	442-448	7
α-helix	465-496	32
α-helix	507-510	4
β-strand	518-525	8	77
α-helix	527-531	5
α-helix	537-542	6
β-strand	550-558	9	77
β-strand	561-569	9	77
β-strand	579-585	7	77
β-strand	590	1	77
α-helix	596-602	7
α-helix	603-607	5
α-helix	609-611	3
α-helix	621-638	18
β-strand	663	1	78
β-strand	668	1	78
α-helix	669-670	2
β-strand	672-674	3	79
β-strand	679-681	3	79

Chains f, F, n and N: 4 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	30-32	3	80
β-strand	38-42	5	80
β-strand	47-52	6	80
α-helix	53-56	4
α-helix	63-65	3
β-strand	70-73	4	80
β-strand	81-84	4	81
β-strand	88-92	5	81
β-strand	97-101	5	81
α-helix	102-105	4
β-strand	112-116	5	81
β-strand	129-135	7	82
β-strand	140-145	6	82
β-strand	150-154	5	82
β-strand	160-164	5	82
β-strand	171-174	4	83
β-strand	184-187	4	83
β-strand	191-196	6	83
β-strand	201-207	7	83
β-strand	223-225	3	84
β-strand	228	1	85
β-strand	232-235	4	85
β-strand	236-237	2	84
β-strand	241-245	5	85
β-strand	250-255	6	85
β-strand	261-266	6	86
β-strand	270-275	6	86
β-strand	279-284	6	86
β-strand	289-294	6	86
β-strand	300-305	6	87
β-strand	317-321	5	87
β-strand	325-329	5	87
β-strand	331	1	88
β-strand	334	1	88
β-strand	337-340	4	87

Chains g and G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-12	6
α-helix	24-40	17
α-helix	46-127	82
α-helix	134-180	47

Chains h and H: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	258	1	89
β-strand	262-268	7	90
α-helix	274-284	11
β-strand	289-293	5	90
α-helix	297-308	12
β-strand	314-317	4	90
α-helix	323-334	12
β-strand	340-343	4	90
β-strand	356-361	6	90
α-helix	368-375	8
β-strand	377	1	89
β-strand	385-391	7	90
α-helix	394-407	14
β-strand	412-413	2	90
α-helix	414	1

Chains i and I: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	11-21	11
α-helix	30-36	7
α-helix	45-64	20
α-helix	71-83	13
α-helix	92-103	12
α-helix	107-118	12
α-helix	134-146	13
α-helix	153-166	14
α-helix	232-246	15
α-helix	248-250	3
α-helix	255-274	20
α-helix	316-332	17
α-helix	347-365	19
α-helix	371-391	21
α-helix	436-442	7
α-helix	490-502	13
α-helix	518-527	10

5 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
RNA	2, 4	RNA	3	Homo sapiens
THO complex subunit 1	A, I, a, i	protein	657	Homo sapiens	Q96FV9 (AlphaFold model)
THO complex subunit 2	B, J, b, j	protein	1593	Homo sapiens	Q8NI27 (AlphaFold model)
THO complex subunit 3	C, K, c, k	protein	351	Homo sapiens	Q96J01 (AlphaFold model)
THO complex subunit 5 homolog	E, M, e, m	protein	683	Homo sapiens	Q13769 (AlphaFold model)
THO complex subunit 6 homolog	F, N, f, n	protein	341	Homo sapiens	Q86W42
THO complex subunit 7 homolog	G, O, g, o	protein	204	Homo sapiens	Q6I9Y2
Spliceosome RNA helicase DDX39B	H, P, h, p	protein	428	Homo sapiens	Q13838
THO complex subunit 4	L, l	protein	257	Homo sapiens	Q86V81

Sequence of entity 1 (2, 4), FASTA

>7ZNK_1 RNA (chains 2, 4)
UUU

Sequence of entity 2 (A, I, a, i), FASTA

>7ZNK_2 THO complex subunit 1 (chains A, I, a, i)
MSPTPPLFSLPEARTRFTKSTREALNNKNIKPLLSTFSQVPGSENEKKCTLDQAFRGILE
EEIINHSSCENVLAIISLAIGGVTEGICTASTPFVLLGDVLDCLPLDQCDTIFTFVEKNV
ATWKSNTFYSAGKNYLLRMCNDLLRRLSKSQNTVFCGRIQLFLARLFPLSEKSGLNLQSQ
FNLENVTVFNTNEQESTLGQKHTEDREEGMDVEEGEMGDEEAPTTCSIPIDYNLYRKFWS
LQDYFRNPVQCYEKISWKTFLKYSEEVLAVFKSYKLDDTQASRKKMEELKTGGEHVYFAK
FLTSEKLMDLQLSDSNFRRHILLQYLILFQYLKGQVKFKSSNYVLTDEQSLWIEDTTKSV
YQLLSENPPDGERFSKMVEHILNTEENWNSWKNEGCPSFVKERTSDTKPTRIIRKRTAPE
DFLGKGPTKKILMGNEELTRLWNLCPDNMEACKSETREHMPTLEEFFEEAIEQADPENMV
ENEYKAVNNSNYGWRALRLLARRSPHFFQPTNQQFKSLPEYLENMVIKLAKELPPPSEEI
KTGEDEDEEDNDALLKENESPDVRRDKPVTGEQIEVFANKLGEQWKILAPYLEMKDSEIR
QIECDSEDMKMRAKQLLVAWQDQEGVHATPENLINALNKSGLSDLAESLTNDNETNS

Sequence of entity 3 (B, J, b, j), FASTA

>7ZNK_3 THO complex subunit 2 (chains B, J, b, j)
MAAAAVVVPAEWIKNWEKSGRGEFLHLCRILSENKSHDSSTYRDFQQALYELSYHVIKGN
LKHEQASNVLSDISEFREDMPSILADVFCILDIETNCLEEKSKRDYFTQLVLACLYLVSD
TVLKERLDPETLESLGLIKQSQQFNQKSVKIKTKLFYKQQKFNLLREENEGYAKLIAELG
QDLSGSITSDLILENIKSLIGCFNLDPNRVLDVILEVFECRPEHDDFFISLLESYMSMCE
PQTLCHILGFKFKFYQEPNGETPSSLYRVAAVLLQFNLIDLDDLYVHLLPADNCIMDEHK
REIAEAKQIVRKLTMVVLSSEKMDEREKEKEKEEEKVEKPPDNQKLGLLEALLKIGDWQH
AQNIMDQMPPYYAASHKLIALAICKLIHITIEPLYRRVGVPKGAKGSPVNALQNKRAPKQ
AESFEDLRRDVFNMFCYLGPHLSHDPILFAKVVRIGKSFMKEFQSDGSKQEDKEKTEVIL
SCLLSITDQVLLPSLSLMDCNACMSEELWGMFKTFPYQHRYRLYGQWKNETYNSHPLLVK
VKAQTIDRAKYIMKRLTKENVKPSGRQIGKLSHSNPTILFDYILSQIQKYDNLITPVVDS
LKYLTSLNYDVLAYCIIEALANPEKERMKHDDTTISSWLQSLASFCGAVFRKYPIDLAGL
LQYVANQLKAGKSFDLLILKEVVQKMAGIEITEEMTMEQLEAMTGGEQLKAEGGYFGQIR
NTKKSSQRLKDALLDHDLALPLCLLMAQQRNGVIFQEGGEKHLKLVGKLYDQCHDTLVQF
GGFLASNLSTEDYIKRVPSIDVLCNEFHTPHDAAFFLSRPMYAHHISSKYDELKKSEKGS
KQQHKVHKYITSCEMVMAPVHEAVVSLHVSKVWDDISPQFYATFWSLTMYDLAVPHTSYE
REVNKLKVQMKAIDDNQEMPPNKKKKEKERCTALQDKLLEEEKKQMEHVQRVLQRLKLEK
DNWLLAKSTKNETITKFLQLCIFPRCIFSAIDAVYCARFVELVHQQKTPNFSTLLCYDRV
FSDIIYTVASCTENEASRYGRFLCCMLETVTRWHSDRATYEKECGNYPGFLTILRATGFD
GGNKADQLDYENFRHVVHKWHYKLTKASVHCLETGEYTHIRNILIVLTKILPWYPKVLNL
GQALERRVHKICQEEKEKRPDLYALAMGYSGQLKSRKSYMIPENEFHHKDPPPRNAVASV
QNGPGGGPSSSSIGSASKSDESSTEETDKSRERSQCGVKAVNKASSTTPKGNSSNGNSGS
NSNKAVKENDKEKGKEKEKEKKEKTPATTPEARVLGKDGKEKPKEERPNKDEKARETKER
TPKSDKEKEKFKKEEKAKDEKFKTTVPNAESKSTQEREREKEPSRERDIAKEMKSKENVK
GGEKTPVSGSLKSPVPRSDIPEPEREQKRRKIDTHPSPSHSSTVKDSLIELKESSAKLYI
NHTPPPLSKSKEREMDKKDLDKSRERSREREKKDEKDRKERKRDHSNNDREVPPDLTKRR
KEENGTMGVSKHKSESPCESPYPNEKDKEKNKSKSSGKEKGSDSFKSEKMDKISSGGKKE
SRHDKEKIEKKEKRDSSGGKEEKKHHKSSDKHR

Sequence of entity 4 (C, K, c, k), FASTA

>7ZNK_4 THO complex subunit 3 (chains C, K, c, k)
MAVPAAAMGPSALGQSGPGSMAPWCSVSSGPSRYVLGMQELFRGHSKTREFLAHSAKVHS
VAWSCDGRRLASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASG
DKTIRIWDVRTTKCIATVNTKGENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQ
FKFEVNEISWNNDNNMFFLTNGNGCINILSYPELKPVQSINAHPSNCICIKFDPMGKYFA
TGSADALVSLWDVDELVCVRCFSRLDWPVRTLSFSHDGKMLASASEDHFIDIAEVETGDK
LWEVQCESPTFTVAWHPKRPLLAFACDDKDGKYDSSREAGTVKLFGLPNDS

Sequence of entity 5 (E, M, e, m), FASTA

>7ZNK_5 THO complex subunit 5 homolog (chains E, M, e, m)
MSSESSKKRKPKVIRSDGAPAEGKRNRSDTEQEGKYYSEEAEVDLRDPGRDYELYKYTCQ
ELQRLMAEIQDLKSRGGKDVAIEIEERRIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEAK
QKVDAYHLQLQNLLYEVMHLQKEITKCLEFKSKHEEIDLVSLEEFYKEAPPDISKAEVTM
GDPHQQTLARLDWELEQRKRLAEKYRECLSNKEKILKEIEVKKEYLSSLQPRLNSIMQAS
LPVQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYGQACDKTLSVAIEGSVDEAKAL
FKPPEDSQDDESDSDAEEEQTTKRRRPTLGVQLDDKRKEMLKRHPLSVMLDLKCKDDSVL
HLTFYYLMNLNIMTVKAKVTTAMELITPISAGDLLSPDSVLSCLYPGDHGKKTPNPANQY
QFDKVGILTLSDYVLELGHPYLWVQKLGGLHFPKEQPQQTVIADHSLSASHMETTMKLLK
TRVQSRLALHKQFASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTIAHEDYMELHFTKDIV
DAGLAGDTNLYYMALIERGTAKLQAAVVLNPGYSSIPPIFQLCLNWKGEKTNSNDDNIRA
MEGEVNVCYKELCGPWPSHQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMCLR
LFRGPSRMKPFKYNHPQGFFSHR

Sequence of entity 6 (F, N, f, n), FASTA

>7ZNK_6 THO complex subunit 6 homolog (chains F, N, f, n)
MERAVPLAVPLGQTEVFQALQRLHMTIFSQSVSPCGKFLAAGNNYGQIAIFSLSSALSSE
AKEESKKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEMLKKGCKELWRRQPPY
RTSLEVPEINALLLVPKENSLILAGGDCQLHTMDLETGTFTRVLRGHTDYIHCLALRERS
PEVLSGGEDGAVRLWDLRTAKEVQTIEVYKHEECSRPHNGRWIGCLATDSDWMVCGGGPA
LTLWHLRSSTPTTIFPIRAPQKHVTFYQDLILSAGQGRCVNQWQLSGELKAQVPGSSPGL
LSLSLNQQPAAPECKVLTAAGNSCRVDVFTNLGYRAFSLSF

Sequence of entity 7 (G, O, g, o), FASTA

>7ZNK_7 THO complex subunit 7 homolog (chains G, O, g, o)
MGAVTDDEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQC
EFSMGKTLLVYDMNLREMENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYD
ALAKVIQHHPDRHETLKELEALGKELEHLSHIKESVEDKLELRRKQFHVLLSTIHELQQT
LENDEKLSEVEEAQEASMETDPKP

Sequence of entity 8 (H, P, h, p), FASTA

>7ZNK_8 Spliceosome RNA helicase DDX39B (chains H, P, h, p)
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAI
VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC
HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALA
RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR
KFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRC
IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF
NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI
SSYIEQTR

Sequence of entity 9 (L, l), FASTA

>7ZNK_9 THO complex subunit 4 (chains L, l)
MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGGAQAAARVNRGGGPIRNRPA
IARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDA
DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL
VTSQIDAQRRPAQSVNRGGMTRNRGAGGFGGGGGTRRGTRGGARGRGRGAGRNSKQQLSA
EELDAQLDAYNARMDTS

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 Q96FV9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7APK 3.3 Å, Structure of the human THO - UAP56 complex
7ZNL 3.45 Å, Structure of the human TREX core THO-UAP56 complex
8R7L 4.12 Å, Cryo-EM structure of the human TREX complex
1WXP Solution structure of the death domain of nuclear matrix protein p84

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