9DLR: Human TREX-2.1 complex

Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to the N-terminal motif of DDX39B(UAP56). Determined by electron microscopy at 3.08 Å resolution. Released 17 Sept 2025.

Method
Electron microscopy
Resolution
3.08 Å
Organism
Homo sapiens
Chains
4
Atoms
5,480
Mol. weight
139.35 kDa
Released
17 Sept 2025

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

Secondary structure: helices and β-sheets

9DLR contains 40 α-helices and 10 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, 3 β-strands

ElementResiduesLengthSheet
α-helix577-59216
α-helix596-61318
α-helix618-63417
α-helix637-65216
α-helix659-67214
α-helix676-6849
α-helix688-6925
α-helix694-70714
α-helix711-7199
α-helix725-74723
β-strand751-75331
α-helix754-7607
α-helix766-7738
β-strand78011
β-strand787-78931
α-helix790-7934
α-helix794-7963
Chain B: 23 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix6-1914
α-helix22-298
α-helix34-363
α-helix47-537
α-helix58-7316
α-helix77-9721
α-helix105-12925
α-helix136-15419
α-helix164-1674
α-helix168-18114
α-helix188-19710
α-helix206-22217
α-helix226-23813
β-strand24112
α-helix245-26117
β-strand265-26623
α-helix2671
α-helix268-2736
α-helix278-2869
α-helix291-30010
α-helix302-3087
α-helix311-3144
α-helix317-33317
β-strand337-33934
α-helix340-34910
α-helix357-37014
β-strand375-37844
β-strand383-38644
Chain C: 2 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand3212
α-helix34-363
β-strand39-4023
α-helix51-6111
Chain D: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix11-133

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Leukocyte receptor cluster member 8Aprotein316Homo sapiensQ96PV6 (AlphaFold model)
PCI domain-containing protein 2Bprotein399Homo sapiensQ5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1Cprotein70Homo sapiensP60896 (AlphaFold model)
Spliceosome RNA helicase DDX39BDprotein428Homo sapiensQ13838 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9DLR_1 Leukocyte receptor cluster member 8 (chains A)
GAMGSRSRKKMAALECEDPERELKKQKRAARFQHGHSRRLRLEPLVLQMSSLESSGADPD
WQELQIVGTCPDITKHYLRLTCAPDPSTVRPVAVLKKSLCMVKCHWKEKQDYAFACEQMK
SIRQDLTVQGIRTEFTVEVYETHARIALEKGDHEEFNQCQTQLKSLYAENLPGNVGEFTA
YRILYYIFTKNSGDITTELAYLTRELKADPCVAHALALRTAWALGNYHRFFRLYCHAPCM
SGYLVDKFADRERKVALKAMIKTFRPALPVSYLQAELAFEGEAACRAFLEPLGLAYTGPD
NSSIDCRLSLAQLSAF
Sequence of entity 2 (B), FASTA
>9DLR_2 PCI domain-containing protein 2 (chains B)
MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDE
MFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFAN
NADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYF
KINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHC
HRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAK
HEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEV
QCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC
Sequence of entity 3 (C), FASTA
>9DLR_3 26S proteasome complex subunit SEM1 (chains C)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 4 (D), FASTA
>9DLR_4 Spliceosome RNA helicase DDX39B (chains D)
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAI
VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC
HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALA
RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR
KFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRC
IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF
NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI
SSYIEQTR

Primary citation

Structural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling. Clarke, B.P., Gao, S., Mei, M. et al. Nat Commun (2025) 16:5471-5471. DOI 10.1038/s41467-025-60547-1 · PubMed

Other PDB entries of the same protein (UniProt Q96PV6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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