9DLP: Human TREX-2 complex

Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56). Determined by electron microscopy at 2.79 Å resolution. Released 4 Jun 2025.

Method
Electron microscopy
Resolution
2.79 Å
Organism
Homo sapiens
Chains
4
Atoms
8,522
Mol. weight
177.01 kDa
Ligands
MG, ADP
Released
4 Jun 2025

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

Secondary structure: helices and β-sheets

9DLP contains 66 α-helices and 21 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: 26 helices, 5 β-strands

ElementResiduesLengthSheet
α-helix604-61916
α-helix643-65210
α-helix657-6593
β-strand66011
β-strand66711
α-helix674-6763
α-helix688-6903
α-helix694-70310
α-helix704-7085
α-helix716-73621
α-helix742-76120
α-helix772-79524
α-helix803-81210
α-helix820-8245
α-helix829-8324
α-helix835-84814
α-helix852-8609
α-helix864-8707
α-helix871-8733
α-helix874-88815
β-strand897-90042
α-helix901-9088
α-helix913-9219
β-strand926-92832
β-strand931-93442
α-helix941-9422
α-helix945-9484
α-helix952-9576
α-helix962-9676
α-helix971-9755
α-helix978-9803
Chain B: 26 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix6-1914
α-helix22-298
α-helix34-374
α-helix47-537
α-helix551
α-helix58-7316
α-helix77-9721
α-helix105-12622
α-helix136-15318
α-helix160-1623
α-helix164-1674
α-helix168-17912
α-helix188-19710
α-helix206-22217
α-helix228-23811
β-strand24113
α-helix245-26117
β-strand265-26624
α-helix268-2736
α-helix278-28811
α-helix291-30010
α-helix302-3087
α-helix311-3144
α-helix315-3173
α-helix318-33316
β-strand337-33935
α-helix340-34910
α-helix357-37014
β-strand375-37845
β-strand383-38645
α-helix395-3973
Chain C: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix20-223
β-strand3213
β-strand39-4024
α-helix51-6212
Chain D: 12 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix11-133
α-helix47-504
α-helix54-6310
α-helix70-8011
β-strand85-8846
α-helix95-10511
β-strand116-11946
α-helix123-13614
β-strand145-14846
β-strand15017
β-strand15217
α-helix154-16310
β-strand168-17146
α-helix173-1819
α-helix187-1893
β-strand192-19656
α-helix198-2036
α-helix205-21713
β-strand223-22866
α-helix236-2416
β-strand247-25046

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Germinal-center associated nuclear proteinAprotein648Homo sapiensO60318 (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
>9DLP_1 Germinal-center associated nuclear protein (chains A)
GAMGSKEAKKETGFVESAESDHMAIPGGNQSVLAPSRIPGVNKEEETESREKKEDSLRGT
PARQSNRSESTDSLGGLSPSEVTAIQCKNIPDYLNDRTILENHFGKIAKVQRIFTRRSKK
LAVVHFFDHASAALARKKGKSLHKDMAIFWHRKKISPNKKPFSLKEKKPGDGEVSPSTED
APFQHSPLGKAAGRTGASSLLNKSSPVKKPSLLKAHQFEGDSFDSASEGSEGLGPCVLSL
STLIGTVAETSKEKYRLLDQRDRIMRQARVKRTDLDKARTFVGTCLDMCPEKERYMRETR
SQLSVFEVVPGTDQVDHAAAVKEYSRSSADQEEPLPHELRPLPVLSRTMDYLVTQIMDQK
EGSLRDWYDFVWNRTRGIRKDITQQHLCDPLTVSLIEKCTRFHIHCAHFMCEEPMSSFDA
KINNENMTKCLQSLKEMYQDLRNKGVFCASEAEFQGYNVLLSLNKGDILREVQQFHPAVR
NSSEVKFAVQAFAALNSNNFVRFFKLVQSASYLNACLLHCYFSQIRKDALRALNFAYTVS
TQRSTIFPLDGVVRMLLFRDCEEATDFLTCHGLTVSDGCVELNRSAFLEPEGLSKTRKSV
FITRKLTVSVGEIVNGGPLPPVPRHTPVCSFNSQNKYIGESLAAELPV
Sequence of entity 2 (B), FASTA
>9DLP_2 PCI domain-containing protein 2 (chains B)
MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDE
MFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFAN
NADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYF
KINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHC
HRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAK
HEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEV
QCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC
Sequence of entity 3 (C), FASTA
>9DLP_3 26S proteasome complex subunit SEM1 (chains C)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 4 (D), FASTA
>9DLP_4 Spliceosome RNA helicase DDX39B (chains D)
GAMGSMAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPE
LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLXPVTGQVS
VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR
ILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI
RPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVK
SVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIER
VNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP
DEIDISSYIEQTR

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21

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 O60318 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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