8U8E: TREX-2 complex in association with Sub2

Cryo-EM structure of the TREX-2 complex in association with Sub2. Determined by electron microscopy at 3.33 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.33 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 9,548
Mol. weight: 171.43 kDa
Released: 5 Feb 2025

Explore 8U8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U8E contains 66 α-helices and 17 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: 29 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	90-96	7
α-helix	103-106	4
α-helix	116-119	4
α-helix	120-122	3
α-helix	126-127	2
β-strand	128	1	1
α-helix	138-153	16
α-helix	157-178	22
α-helix	206-215	10
α-helix	247-251	5
α-helix	258-271	14
α-helix	273-275	3
α-helix	280-297	18
β-strand	299	1	1
α-helix	302-325	24
α-helix	331-354	24
α-helix	362-372	11
α-helix	378-385	8
α-helix	388-391	4
α-helix	394-406	13
α-helix	426-433	8
α-helix	440-446	7
α-helix	447-449	3
α-helix	450-462	13
α-helix	469-471	3
β-strand	472-473	2	2
α-helix	474-481	8
α-helix	486-495	10
β-strand	500-501	2	2
β-strand	505-506	2	2
α-helix	508-510	3
α-helix	522-526	5
α-helix	530-536	7
α-helix	541-546	6

Chain B: 26 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	23-25	3
α-helix	27-37	11
α-helix	42-51	10
α-helix	59-74	16
α-helix	84-99	16
α-helix	106-128	23
α-helix	141-154	14
α-helix	170-173	4
α-helix	175-188	14
α-helix	192-194	3
α-helix	195-205	11
α-helix	211-213	3
α-helix	216-232	17
α-helix	236-250	15
α-helix	255-257	3
α-helix	260-277	18
β-strand	282	1	3
α-helix	293-307	15
α-helix	311-320	10
α-helix	322-327	6
α-helix	331-351	21
α-helix	352-356	5
β-strand	362-364	3	4
α-helix	365-376	12
α-helix	400-410	11
β-strand	415-418	4	4
β-strand	423-426	4	4
α-helix	439-446	8
α-helix	448-451	4

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	60	1	3
α-helix	72-87	16

Chain D: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	71-80	10
α-helix	87-98	12
β-strand	102-105	4	5
α-helix	112-123	12
β-strand	133-136	4	5
α-helix	140-153	14
α-helix	154-156	3
β-strand	162-165	4	5
α-helix	171-179	9
β-strand	187-190	4	5
α-helix	192-200	9
β-strand	211-215	5	5
α-helix	217-222	6
α-helix	224-236	13
β-strand	242-247	6	5
α-helix	254-260	7
β-strand	266-268	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear mRNA export factor	A	protein	497	Saccharomyces cerevisiae	P46674 (AlphaFold model)
THP1 isoform 1	B	protein	455	Saccharomyces cerevisiae	Q08231 (AlphaFold model)
26S proteasome complex subunit SEM1	C	protein	89	Saccharomyces cerevisiae	O94742 (AlphaFold model)
RNA helicase	D	protein	446	Saccharomyces cerevisiae	Q07478 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8U8E_1 Nuclear mRNA export factor (chains A)
GAMGSKSQQPLQNLSHSPSYTENKPDKKKKYMINDAKTIQLVGPLISSPDNLGFQKRSHK
ARELPRFLINQEPQLEKRAFVQDPWDKANQEKMISLEESIDDLNELYETLKKMRNTERSI
MEEKGLVDKADSAKDLYDAIVFQGTCLDMCPTFERSRRNVEYTVYSYEKNQPNDKKASRT
KALKVFARPAAAAAPPLPSDVRPPHILVKTLDYIVDNLLTTLPESEGFLWDRMRSIRQDF
TYQNYSGPEAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYDDVRS
SGGTCPNEAEFRAYALLSKIRDPQYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTER
GFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPF
IYLENMLLFNNRQEIIEFCNYYSIEIINGDAADLKTLQHYSHKLSETQPLKKTYLTCLER
RLQKTTYKGLINGGEDN

Sequence of entity 2 (B), FASTA

>8U8E_2 THP1 isoform 1 (chains B)
MDMANQLLDELAHGNFSHLTLNLSQNGREIAILQKQLTGFDDKQLETFVEQHPAMPNDTR
FKIMCTSFLNYARDVDPWSAWSSSDLIFEFYQCLINCLINDNAPHIEMLIPVATRETEFI
INLAGKLDSFHLQLHTRSHQFLSHISSILSRLFNSIKPPRGNASSTNIPGKQRILLYLVN
KLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNSQVHNAF
VQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVKWGPLRPFLSQETIDNWS
VLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTEWGQ
NKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLINLGLLRANCFPQ
LQLCVVKKTTMIQEIVPPVNERITKMFPAHSHVLW

Sequence of entity 3 (C), FASTA

>8U8E_3 26S proteasome complex subunit SEM1 (chains C)
MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIW
EENWDDVEVDDDFTNELKAELDRYKRENQ

Sequence of entity 4 (D), FASTA

>8U8E_4 RNA helicase (chains D)
MSHEGEEDLLEYSDNEQEIQIDASKAAEAGETGAATSATEGDNNNNTAAGDKKGSYVGIH
STGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAVFVLST
LQQLXPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDAELLKN
KDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFRATPRD
KQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNRKLAQL
LDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDFEKRIC
VSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKEDEEVLA
KIQERFDVKIAEFPEEGIDPSTYLNN

Primary citation

Structures and mRNP remodeling mechanism of the TREX-2 complex. Xie, Y., Clarke, B.P., Xie, D. et al. Structure (2025) 33:566-582.e6. DOI 10.1016/j.str.2024.12.019 · PubMed

Other PDB entries of the same protein (UniProt P46674 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8U8C 2.4 Å, Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
3FWB 2.5 Å, Sac3:Sus1:Cdc31 complex
4MBE 2.61 Å, Sac3:Sus1:Cdc31:Nup1 complex
3FWC 2.7 Å, Sac3:Sus1:Cdc31 complex
3T5V 2.9 Å, Sac3:Thp1:Sem1 complex
4C31 3.0 Å, Nup1:Sac3:Sus1 complex
8U8D 3.04 Å, Cryo-EM structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
4TRQ 3.1 Å, Crystal structure of Sac3/Thp1/Sem1
5L3T 4.93 Å, Structure of the Saccharomyces cerevisiae TREX-2 complex
5G5P 5.3 Å, Structure of the Saccharomyces cerevisiae TREX-2 complex

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