9T6N: Human GANP-PCID2-DSS1 complex

Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56. Determined by electron microscopy at 3.0 Å resolution. Released 27 May 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,254
Mol. weight: 150.97 kDa
Ligands: ADP, MG
Released: 27 May 2026

Explore 9T6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T6N contains 61 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 B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
α-helix	54-62	9
α-helix	70-81	12
β-strand	85-88	4	1
α-helix	95-106	12
β-strand	116-119	4	1
α-helix	123-136	14
β-strand	145-148	4	1
α-helix	155-163	9
β-strand	168-171	4	1
α-helix	173-181	9
β-strand	192-196	5	1
α-helix	199-202	4
α-helix	207-216	10
β-strand	223-228	6	1
α-helix	236-239	4
α-helix	240-242	3
β-strand	247-250	4	1

Chain C: 25 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	104-120	17
α-helix	128-130	3
α-helix	144-153	10
β-strand	161	1	2
α-helix	167	1
β-strand	168	1	2
α-helix	169	1
α-helix	170-172	3
α-helix	186-188	3
α-helix	189-191	3
α-helix	195-208	14
α-helix	217-237	21
α-helix	245-262	18
α-helix	273-295	23
α-helix	305-313	9
α-helix	321-325	5
α-helix	330-333	4
α-helix	336-349	14
α-helix	353-360	8
α-helix	365-371	7
α-helix	372-374	3
α-helix	375-389	15
β-strand	398-401	4	3
α-helix	402-409	8
α-helix	414-422	9
β-strand	427-429	3	3
β-strand	432-435	4	3
α-helix	453-456	4
α-helix	463-468	6
α-helix	472-476	5
β-strand	484	1	4
β-strand	490	1	4

Chain D: 23 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	22-27	6
α-helix	49-52	4
α-helix	58-72	15
α-helix	77-95	19
α-helix	105-125	21
α-helix	137-153	17
α-helix	164-167	4
α-helix	168-182	15
α-helix	188-197	10
α-helix	206-222	17
α-helix	226-238	13
β-strand	241	1	5
α-helix	245-260	16
β-strand	265-266	2	6
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	314-317	4
α-helix	318-333	16
β-strand	337-339	3	7
α-helix	340-349	10
α-helix	357-370	14
β-strand	375-378	4	7
β-strand	383-386	4	7
α-helix	395-397	3

Chain E: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
β-strand	32	1	5
β-strand	39-40	2	6
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)
Germinal-center associated nuclear protein	C	protein	405	Homo sapiens	O60318 (AlphaFold model)
PCI domain-containing protein 2	D	protein	403	Homo sapiens	Q5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1	E	protein	70	Homo sapiens	P60896 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9T6N_1 Spliceosome RNA helicase DDX39B (chains B)
GPDSMAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPEL
LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSV
LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI
LALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR
PVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKS
VQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERV
NIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD
EIDISSYIEQTR

Sequence of entity 2 (C), FASTA

>9T6N_2 Germinal-center associated nuclear protein (chains C)
GPDMTVAETSKEKYRLLDQRDRIMRQARVKRTDLDKARTFVGTCLDMCPEKERYMRETRS
QLSVFEVVPGTDQVDHAAAVKEYSRSSADQEEPLPHELRPLPVLSRTMDYLVTQIMDQKE
GSLRDWYDFVWNRTRGIRKDITQQHLCDPLTVSLIEKCTRFHIHCAHFMCEEPMSSFDAK
INNENMTKCLQSLKEMYQDLRNKGVFCASEAEFQGYNVLLSLNKGDILREVQQFHPAVRN
SSEVKFAVQAFAALNSNNFVRFFKLVQSASYLNACLLHCYFSQIRKDALRALNFAYTVST
QRSTIFPLDGVVRMLLFRDCEEATDFLTCHGLTVSDGCVELNRSAFLEPEGLSKTRKSVF
ITRKLTVSVGEIVNGGPLPPVPRHTPVCSFNSQNKYIGESLAAEL

Sequence of entity 3 (D), FASTA

>9T6N_3 PCI domain-containing protein 2 (chains D)
MGSSMAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEP
PYDEMFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLR
VFANNADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLF
KIYFKINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFA
FEHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHE
ALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVD
IDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Sequence of entity 4 (E), FASTA

>9T6N_4 26S proteasome complex subunit SEM1 (chains E)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

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)
9T6L 2.9 Å, Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B
9DLV 2.97 Å, Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(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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