9ZEB: TREX-2.1 complex

Cryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound to the DEAD-box ATPase Sub2. Determined by electron microscopy at 3.72 Å resolution. Released 30 Sept 2026.

Method
Electron microscopy
Resolution
3.72 Å
Organism
Saccharomyces cerevisiae
Chains
4
Atoms
7,777
Mol. weight
151.51 kDa
Ligands
ADP
Released
30 Sept 2026

Explore 9ZEB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZEB contains 51 α-helices and 20 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: 14 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix215-23016
α-helix236-25116
α-helix258-27417
α-helix277-29115
α-helix301-31414
α-helix318-33114
α-helix334-3374
α-helix340-35415
α-helix357-3648
α-helix369-39325
β-strand39411
β-strand397-39822
α-helix399-4057
α-helix413-4208
α-helix424-4263
β-strand427-43372
β-strand439-44572
α-helix447-45711
Chain B: 23 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-433
α-helix5-117
α-helix18-225
α-helix27-293
β-strand33-3533
α-helix44-6825
α-helix75-9723
α-helix102-1043
α-helix105-12117
α-helix129-14517
α-helix157-1593
α-helix160-17314
α-helix177-19216
α-helix208-2103
α-helix211-22414
α-helix229-24113
β-strand24414
α-helix2541
α-helix257-27317
β-strand278-27925
α-helix284-2907
α-helix300-30910
α-helix312-32110
α-helix323-3286
α-helix332-35423
β-strand360-36231
α-helix363-3675
α-helix380-39718
β-strand402-40541
β-strand410-41341
Chain C: 2 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand4814
α-helix49-535
β-strand60-6125
α-helix72-8716
Chain D: 12 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix64-674
α-helix71-8010
α-helix87-9711
β-strand102-10436
α-helix112-12211
β-strand133-13646
α-helix140-15314
α-helix154-1563
β-strand162-16436
α-helix171-1799
β-strand187-19046
α-helix192-20110
β-strand211-21556
α-helix217-2226
α-helix224-23411
β-strand242-24656
α-helix254-2585
α-helix259-2613
β-strand266-26836

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein THP3Aprotein336Saccharomyces cerevisiaeQ12049 (AlphaFold model)
Cop9 signalosome complex subunit 12Bprotein429Saccharomyces cerevisiaeP47130 (AlphaFold model)
26S proteasome complex subunit SEM1Cprotein93Saccharomyces cerevisiaeO94742 (AlphaFold model)
ATP-dependent RNA helicase SUB2Dprotein451Saccharomyces cerevisiaeQ07478 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9ZEB_1 Protein THP3 (chains A)
GAMGSDELERRKRRAERFSQGPSATTNSNDNLNEDFANLNAISSKSHQYDKKIHVVGRCQ
TLEKSYLRLTSEPNPDLIRPPNILQKMYCLLMDKYQSKTATYTYLCDQFKSMRQDLRVQM
IENSFTIKVYQTHARIALENGDLGEFNQCQNRIMALFENPTIPKKSYSEFICYSVLYSML
TEDYPSISHLKLKLIDDGSSEILEDEHVKMIFELSDMKLVGNYHYFMKNYLKLHKFEKCL
INSFLNLEKLIFLTIICKSYNQVNLDFVKSEFNFNSIEETTNFLNEQNLTEFILNKQITD
SNGKSSNIKILNTKGCRVQLIQNYMKSKKIDIKGQK
Sequence of entity 2 (B), FASTA
>9ZEB_2 Cop9 signalosome complex subunit 12 (chains B)
GADPNSMDVDIGCYFEEKRYDDKLLDFIRYDVKTPKKTKYILQRPTATDEESVRLQRFYQ
LGVDLKLKYSKRRSLKKQGRIKNATEELLRLANEQLKLFNRIVERETNWIIYPLWVMAKQ
LIRLANESSELNKDSIEECGRTIHRSFTICLNDRNPRLNENKKIGCYMFANLEFSIYHRL
SNKDMIKNLVKVLESRVNARDIPPLNKSLAMEHKSQVVLYNYYLGQYYGCLENDHERGFF
HLNEALLQCPMLYVESTGKFVLQGQMEKIMILLVPLALLTKRLYPHWDHPVIAGVITRSK
RLSQVYPTLVRSVISGNLSLYEATAASHERFFLSQGLHVVITLLREVVFTRLVQRCWQWG
NDRKSIMPLKILLATKQHDSSANEDEEEQLDALECRLASAIASGLLRAYLSHSNRCIVFS
KKEPFPHSK
Sequence of entity 3 (C), FASTA
>9ZEB_3 26S proteasome complex subunit SEM1 (chains C)
MADLMSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQ
TNIWEENWDDVEVDDDFTNELKAELDRYKRENQ
Sequence of entity 4 (D), FASTA
>9ZEB_4 ATP-dependent RNA helicase SUB2 (chains D)
GAMGSMSHEGEEDLLEYSDNEQEIQIDASKAAEAGETGAATSATEGDNNNNTAAGDKKGS
YVGIHSTGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAV
FVLSTLQQLXPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDA
ELLKNKDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFR
ATPRDKQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNR
KLAQLLDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDF
EKRICVSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKED
EEVLAKIQERFDVKIAEFPEEGIDPSTYLNN

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21

Primary citation

Conserved mRNP remodeling mechanism of the TREX-2.1 complex. Angelos, A.E., Asada, R., Clarke, B.P. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag884 · PubMed

Other PDB entries of the same protein (UniProt Q12049 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 9ZEB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.