9DLV: Human TREX-2.1 complex

Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(UAP56). Determined by electron microscopy at 2.97 Å resolution. Released 17 Sept 2025.

Method
Electron microscopy
Resolution
2.97 Å
Organism
Homo sapiens
Chains
4
Atoms
7,245
Mol. weight
139.86 kDa
Released
17 Sept 2025

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

Secondary structure: helices and β-sheets

9DLV contains 51 α-helices and 18 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-helix576-59318
α-helix596-61217
α-helix618-63316
α-helix637-65216
α-helix659-67315
α-helix676-6849
α-helix688-6914
α-helix694-70714
α-helix711-7199
α-helix725-74521
β-strand74811
β-strand752-75322
α-helix754-7607
α-helix766-7738
α-helix774-7763
β-strand78112
β-strand787-78822
α-helix790-79910
Chain B: 24 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix6-1813
α-helix22-276
α-helix34-374
α-helix551
α-helix58-7316
α-helix77-9721
α-helix105-12925
α-helix136-15318
α-helix160-1623
α-helix164-1674
α-helix168-18215
α-helix185-1873
α-helix188-19710
α-helix206-22217
α-helix226-23813
β-strand24113
α-helix245-26218
β-strand265-26624
α-helix268-2736
α-helix280-2889
α-helix291-30010
α-helix302-3087
α-helix311-3144
α-helix317-33317
β-strand337-33931
α-helix342-3498
α-helix357-36913
β-strand375-37731
β-strand383-38641
Chain C: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix20-223
β-strand3213
β-strand39-4024
α-helix51-6212
Chain D: 11 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix11-133
α-helix47-504
α-helix54-6310
α-helix70-8011
β-strand85-8845
α-helix95-10511
β-strand116-12055
α-helix123-13513
β-strand145-14845
α-helix154-16310
β-strand168-17145
α-helix173-1819
β-strand192-19655
α-helix198-2036
α-helix206-21712
β-strand223-22865
α-helix235-2406
β-strand247-25045

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 DDX39BDprotein433Homo sapiensQ13838 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9DLV_1 Leukocyte receptor cluster member 8 (chains A)
GAMGSRSRKKMAALECEDPERELKKQKRAARFQHGHSRRLRLEPLVLQMSSLESSGADPD
WQELQIVGTCPDITKHYLRLTCAPDPSTVRPVAVLKKSLCMVKCHWKEKQDYAFACEQMK
SIRQDLTVQGIRTEFTVEVYETHARIALEKGDHEEFNQCQTQLKSLYAENLPGNVGEFTA
YRILYYIFTKNSGDITTELAYLTRELKADPCVAHALALRTAWALGNYHRFFRLYCHAPCM
SGYLVDKFADRERKVALKAMIKTFRPALPVSYLQAELAFEGEAACRAFLEPLGLAYTGPD
NSSIDCRLSLAQLSAF
Sequence of entity 2 (B), FASTA
>9DLV_2 PCI domain-containing protein 2 (chains B)
MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDE
MFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFAN
NADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYF
KINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHC
HRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAK
HEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEV
QCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC
Sequence of entity 3 (C), FASTA
>9DLV_3 26S proteasome complex subunit SEM1 (chains C)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 4 (D), FASTA
>9DLV_4 Spliceosome RNA helicase DDX39B (chains D)
GAMGSMAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPE
LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLXPVTGQVS
VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR
ILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI
RPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVK
SVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER
VNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP
DEIDISSYIEQTR

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:

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