9T6L: Human LENG8-PCID2-DSS1 complex

Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B. Determined by electron microscopy at 2.9 Å resolution. Released 27 May 2026.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,400
Mol. weight: 135.01 kDa
Released: 27 May 2026

Explore 9T6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T6L contains 44 α-helices and 12 β-strands across 3 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 C: 15 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	576-590	15
α-helix	596-613	18
α-helix	618-634	17
α-helix	637-651	15
α-helix	660-672	13
α-helix	676-683	8
α-helix	688-691	4
α-helix	694-708	15
α-helix	711-719	9
α-helix	725-729	5
α-helix	733-747	15
β-strand	748	1	1
β-strand	753	1	2
α-helix	754-760	7
α-helix	766-773	8
α-helix	774-776	3
β-strand	780	1	3
β-strand	787	1	2
β-strand	788	1	3
α-helix	815-818	4

Chain D: 27 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	24-29	6
α-helix	34-37	4
α-helix	39-41	3
α-helix	46-48	3
α-helix	59-73	15
α-helix	78-95	18
α-helix	105-126	22
α-helix	138-153	16
α-helix	160-162	3
α-helix	168-182	15
α-helix	188-197	10
α-helix	206-221	16
α-helix	228-238	11
β-strand	241	1	4
α-helix	245-261	17
α-helix	264	1
β-strand	265-266	2	5
α-helix	267	1
α-helix	268-273	6
α-helix	277-279	3
α-helix	280-288	9
α-helix	291-300	10
α-helix	302-308	7
α-helix	311-314	4
α-helix	315-317	3
α-helix	318-333	16
β-strand	337-339	3	1
α-helix	340-349	10
α-helix	357-370	14
β-strand	375-378	4	1
β-strand	383-386	4	1

Chain E: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	4
α-helix	33-34	2
β-strand	39-40	2	5
α-helix	51-62	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spliceosome RNA helicase DDX39B	B	protein	432	Homo sapiens	Q13838 (AlphaFold model)
Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B	C	protein	273	Homo sapiens	Q14684 (AlphaFold model), Q96PV6 (AlphaFold model)
PCI domain-containing protein 2	D	protein	402	Homo sapiens	Q5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1	E	protein	70	Homo sapiens	P60896

Sequence of entity 1 (B), FASTA

>9T6L_1 Spliceosome RNA helicase DDX39B (chains B)
GPDSMAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL
LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV
LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI
LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR
PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS
VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV
NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD
EIDISSYIEQTR

Sequence of entity 2 (C), FASTA

>9T6L_2 Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B (chains C)
GPDIVGTCPDITKHYLRLTCAPDPSTVRPVAVLKKSLCMVKCHWKEKQDYAFACEQMKSI
RQDLTVQGIRTEFTVEVYETHARIALEKGDHEEFNQCQTQLKSLYAENLPGNVGEFTAYR
ILYYIFTKNSGDITTELAYLTRELKADPCVAHALALRTAWALGNYHRFFRLYCHAPCMSG
YLVDKFADRERKVALKAMIKTFRPALPVSYLQAELAFEGEAACRAFLEPLGLAYTGPDNS
SIDCRLSLAQLSAFGSKPLTTTPRRRPRAMDFF

Sequence of entity 3 (D), FASTA

>9T6L_3 PCI domain-containing protein 2 (chains D)
MGSMAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPP
YDEMFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRV
FANNADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFK
IYFKINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAF
EHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEA
LAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDI
DEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Sequence of entity 4 (E), FASTA

>9T6L_4 26S proteasome complex subunit SEM1 (chains E)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Primary citation

Evolutionarily conserved spliceosome-exosome pathway in nuclear mRNA surveillance. Abbas, D.K., Bonneau, F., Wilkinson, M.E. et al. Genes Dev (2026) 40:1119-1132. DOI 10.1101/gad.353594.125 · PubMed

Other PDB entries of the same protein (UniProt Q13838 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1T5I 1.9 Å, Crystal structure of the C-terminal domain of UAP56
1T6N 1.94 Å, Crystal structure of the N-terminal domain of human UAP56
1XTI 1.95 Å, Structure of Wildtype human UAP56
1XTK 2.4 Å, structure of DECD to DEAD mutation of human UAP56
8ENK 2.5 Å, Crystal structure of UAP56 in complex with Tho1, the yeast homolog of human SARNP
9RV1 2.62 Å, Cryo-EM structure of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
1XTJ 2.7 Å, structure of human UAP56 in complex with ADP
9DLP 2.79 Å, Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)
9DLV 2.97 Å, Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(UAP56)
9T6N 3.0 Å, Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56
9DLR 3.08 Å, Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to the…
7APK 3.3 Å, Structure of the human THO - UAP56 complex

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