5L3T: Saccharomyces cerevisiae TREX-2 complex
Structure of the Saccharomyces cerevisiae TREX-2 complex. Determined by X-ray diffraction at 4.93 Å resolution. Released 27 Jul 2016.
- Method
- X-ray diffraction
- Resolution
- 4.93 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 6
- Atoms
- 6,831
- Mol. weight
- 218.07 kDa
- Released
- 27 Jul 2016
Explore 5L3T in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5L3T contains 55 α-helices and 8 β-strands across 6 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: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 258-271 | 14 | |
| α-helix | 273-279 | 7 | |
| α-helix | 280-296 | 17 | |
| α-helix | 302-324 | 23 | |
| α-helix | 332-354 | 23 | |
| α-helix | 362-372 | 11 | |
| α-helix | 377-384 | 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 | 1 |
| α-helix | 474-481 | 8 | |
| α-helix | 486-495 | 10 | |
| β-strand | 500-501 | 2 | 1 |
| β-strand | 505-506 | 2 | 1 |
| α-helix | 508-510 | 3 | |
| α-helix | 522-526 | 5 | |
| α-helix | 530-536 | 7 | |
| α-helix | 541-545 | 5 | |
Chain B: 29 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-12 | 10 | |
| α-helix | 23-37 | 15 | |
| α-helix | 42-50 | 9 | |
| α-helix | 59-74 | 16 | |
| α-helix | 84-96 | 13 | |
| α-helix | 106-128 | 23 | |
| α-helix | 131-134 | 4 | |
| α-helix | 140-155 | 16 | |
| α-helix | 156-160 | 5 | |
| α-helix | 170-173 | 4 | |
| α-helix | 175-188 | 14 | |
| α-helix | 192-194 | 3 | |
| α-helix | 195-200 | 6 | |
| α-helix | 202-205 | 4 | |
| α-helix | 211-213 | 3 | |
| α-helix | 216-232 | 17 | |
| α-helix | 236-252 | 17 | |
| α-helix | 258-277 | 20 | |
| β-strand | 282 | 1 | 2 |
| α-helix | 288-290 | 3 | |
| α-helix | 293-308 | 16 | |
| α-helix | 311-320 | 10 | |
| α-helix | 322-327 | 6 | |
| α-helix | 331-351 | 21 | |
| α-helix | 352-357 | 6 | |
| β-strand | 362-364 | 3 | 3 |
| α-helix | 365-376 | 12 | |
| α-helix | 400-409 | 10 | |
| β-strand | 415-418 | 4 | 3 |
| β-strand | 423-426 | 4 | 3 |
| α-helix | 432-435 | 4 | |
| α-helix | 439-446 | 8 | |
| α-helix | 448-451 | 4 | |
Chain C: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| α-helix | 35-37 | 3 | |
| β-strand | 60 | 1 | 2 |
| α-helix | 72-87 | 16 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-16 | 15 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-23 | 21 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-10 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Nuclear mRNA export protein SAC3 | A | protein | 1301 | Saccharomyces cerevisiae | P46674 (AlphaFold model) |
| Nuclear mRNA export protein THP1 | B | protein | 455 | Saccharomyces cerevisiae | Q08231 (AlphaFold model) |
| 26S proteasome complex subunit SEM1 | C | protein | 89 | Saccharomyces cerevisiae | O94742 (AlphaFold model) |
| Sac3polyAla | D, E | protein | 24 | Saccharomyces cerevisiae | |
| Sac3polyAla | F | protein | 12 | Saccharomyces cerevisiae | |
Sequence of entity 1 (A), FASTA
>5L3T_1 Nuclear mRNA export protein SAC3 (chains A)
MNTSFGSVVPSTNFNFFKGHGNNDNTSANSTVNNSNFFLNSNETKPSKNVFMVHSTSQKK
SQQPLQNLSHSPSYTENKPDKKKKYMINDAKTIQLVGPLISSPDNLGFQKRSHKARELPR
FLINQEPQLEKRAFVQDPWDKANQEKMISLEESIDDLNELYETLKKMRNTERSIMEEKGL
VDKADSAKDLYDAIVFQGTCLDMCPTFERSRRNVEYTVYSYEKNQPNDKKASRTKALKVF
ARPAAAAAPPLPSDVRPPHILVKTLDYIVDNLLTTLPESEGFLWDRMRSIRQDFTYQNYS
GPEAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYDDVRSSGGTCP
NEAEFRAYALLSKIRDPQYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTE
NCLNFYARFFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPFIYLENM
LLFNNRQEIIEFCNYYSIEIINGDAADLKTLQHYSHKLSETQPLKKTYLTCLERRLQKTT
YKGLINGGEDNLASSVYVKDPKKDRIPSIADQSFLMENFQNNYNEKLNQNSSVKPQINTS
PKRVATRPNHFPFSQESKQLPQISQSHTLSTNPLLTPQVHGDLSEQKQQQIKTVTDGGSP
FVFDQSAQNSTVEASKAHMISTTSNGAYDEKLSSEQEEMRKKEEQRIEEEKTQLKKKQEN
ADKQVITEQIANDLVKEVVNSSVISIVKREFSEANYRKDFIDTMTRELYDAFLHERLYLI
YMDSRAELKRNSTLKKKFFEKWQASYSQAKKNRILEEKKREEIKLVSHQLGVPGFKKSTC
LFRTPYKGNVNSSFMLSSSDKNLIFSPVNDEFNKFATHLTKISKLWRPLEMQSIYYDNLT
KKFPSNSLTPANLFIYAKDWTSLSNRWILSKFNLQTAQDSKKFSNNIISSRIICIDDEYE
PSDFSDLQLLIFNTGVTNPDIFDLEMKLKDDGEELIKLITGISLNTNICFSLLIIYWESA
ENTLSESTIKHLLKLNRISKNYSSVIERIDLMNLTEESPHKCLEDKLSEISHSYVYKLTE
RGKYDKTLRQKRSLAGIHSRSTQLQTTKDIDQKMKKMLEKEKNKYQQQIGERNTYAHLES
HIDASPRSKKRKLPILLSTSHSSQFKTPLASRLNTSGSSTSPPLPSHLAMKFRKNSRVTS
LHTVLPVSTPSHSNNIPAASFSGNNTTDIQSQQLIENQKSTSVYLNNVSERILGNQEICQ
TPINPVTPVLDGADQGKEDIPDSILELKILIDSVKKKVNND
Sequence of entity 2 (B), FASTA
>5L3T_2 Nuclear mRNA export protein THP1 (chains B)
MDMANQLLDELAHGNFSHLTLNLSQNGREIAILQKQLTGFDDKQLETFVEQHPAMPNDTR
FKIMCTSFLNYARDVDPWSAWSSSDLIFEFYQCLINCLINDNAPHIEMLIPVATRETEFI
INLAGKLDSFHLQLHTRSHQFLSHISSILSRLFNSIKPPRGNASSTNIPGKQRILLYLVN
KLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNSQVHNAF
VQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVKWGPLRPFLSQETIDNWS
VLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTEWGQ
NKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLINLGLLRANCFPQ
LQLCVVKKTTMIQEIVPPVNERITKMFPAHSHVLW
Sequence of entity 3 (C), FASTA
>5L3T_3 26S proteasome complex subunit SEM1 (chains C)
MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIW
EENWDDVEVDDDFTNELKAELDRYKRENQ
Sequence of entity 4 (D, E), FASTA
>5L3T_4 Sac3polyAla (chains D, E)
XXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 5 (F), FASTA
>5L3T_5 Sac3polyAla (chains F)
XXXXXXXXXXXX
Primary citation
The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region. Aibara, S., Bai, X.C., Stewart, M. J Struct Biol (2016) 195:316-324. DOI 10.1016/j.jsb.2016.07.007 · 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
- 8U8E 3.33 Å, Cryo-EM structure of the TREX-2 complex in association with Sub2
- 5G5P 5.3 Å, Structure of the Saccharomyces cerevisiae TREX-2 complex
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