28XB: Human UAP56-RNA - LENG8-PCID2-SEM1 complex

Cryo-EM structure of the human UAP56-RNA - LENG8-PCID2-SEM1 complex. Determined by electron microscopy at 6.2 Å resolution. Released 24 Jun 2026.

Method
Electron microscopy
Resolution
6.2 Å
Organisms
Escherichia coli, Homo sapiens
Chains
5
Atoms
5,453
Mol. weight
185.21 kDa
Released
24 Jun 2026

Explore 28XB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28XB contains 65 α-helices and 24 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: 17 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix567-5693
α-helix574-5752
α-helix576-59217
α-helix596-61318
α-helix618-63417
α-helix637-65317
α-helix659-67315
α-helix676-68510
α-helix688-6925
α-helix694-6985
α-helix700-7089
α-helix711-72010
α-helix725-74723
β-strand74811
β-strand751-75332
α-helix754-7607
α-helix766-77611
β-strand780-78122
α-helix783-7853
β-strand787-78932
α-helix790-79910
Chain B: 24 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix8-1912
α-helix22-298
α-helix49-535
α-helix58-7316
α-helix77-9721
α-helix101-12828
α-helix136-15318
α-helix164-1663
α-helix168-18215
α-helix185-19713
α-helix199-2013
α-helix206-22217
α-helix226-23914
α-helix245-26117
β-strand265-26623
α-helix2671
α-helix268-2736
α-helix277-28812
α-helix291-30010
α-helix302-3087
α-helix310-33324
β-strand337-33931
α-helix340-34910
α-helix357-36913
β-strand377-37821
α-helix379-3813
β-strand383-38531
α-helix395-3984
Chain C: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix34-385
β-strand39-4023
α-helix41-433
α-helix51-6313
Chain H: 21 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix11-133
α-helix47-504
α-helix54-6310
α-helix70-8011
β-strand85-8844
α-helix95-10612
β-strand116-11945
β-strand12014
α-helix123-13614
α-helix137-1393
β-strand145-14735
α-helix154-16310
β-strand168-17145
α-helix173-1819
α-helix187-1893
β-strand192-19654
α-helix198-2036
α-helix205-21713
β-strand223-22754
α-helix235-2428
α-helix2461
β-strand247-25044
β-strand262-26876
α-helix271-28414
β-strand290-29346
α-helix297-30913
β-strand314-31636
α-helix323-33412
β-strand340-34346
α-helix345-3484
β-strand359-36136
α-helix368-3769
β-strand385-39176
α-helix394-40714
β-strand412-41326
α-helix4141

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Maltose/maltodextrin-binding periplasmic protein,Leukocyte receptor cluster member 8,Leukocyte…Aprotein688Escherichia coli, Homo sapiensQ96PV6 (AlphaFold model)
PCI domain-containing protein 2Bprotein456Homo sapiensQ5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1Cprotein49Homo sapiensP60896 (AlphaFold model)
Spliceosome RNA helicase DDX39BHprotein428Homo sapiensQ13838 (AlphaFold model)
RNA (5'-r(p*up*up*up*up*up*u)-3')1RNA6Homo sapiens
Sequence of entity 1 (A), FASTA
>28XB_1 Maltose/maltodextrin-binding periplasmic protein,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8,Leukocyte receptor cluster member 8 (chains A)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDE
ALKDAQTSSGLEVLFQGPSRKKMAALECEDPERELKKQKRAARFQHGHSRRLRLEPLVLQ
MSSLESSGADPDWQELQIVGTCPDITKHYLRLTCAPDPSTVRPVAVLKKSLCMVKCHWKE
KQDYAFACEQMKSIRQDLTVQGIRTEFTVEVYETHARIALEKGDHEEFNQCQTQLKSLYA
ENLPGNVGEFTAYRILYYIFTKNSGDITTELAYLTRELKADPCVAHALALRTAWALGNYH
RFFRLYCHAPCMSGYLVDKFADRERKVALKAMIKTFRPALPVSYLQAELAFEGEAACRAF
LEPLGLAYTGPDNSSIDCRLSLAQLSAF
Sequence of entity 2 (B), FASTA
>28XB_2 PCI domain-containing protein 2 (chains B)
GKPIPNPLLGLDSTGSGKPIPNPLLGLDSTGSGKPIPNPLLGLDSTSSGLEVLFQGPMAH
ITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDEMFA
AHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFANNAD
QQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYFKIN
KLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRS
SQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEA
FFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCI
LANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC
Sequence of entity 3 (C), FASTA
>28XB_3 26S proteasome complex subunit SEM1 (chains C)
FPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMETS
Sequence of entity 4 (H), FASTA
>28XB_4 Spliceosome RNA helicase DDX39B (chains H)
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAI
VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC
HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALA
RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR
KFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRC
IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF
NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI
SSYIEQTR
Sequence of entity 5 (1), FASTA
>28XB_5 RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') (chains 1)
UUUUUU

Primary citation

Molecular basis of polyadenylated RNA fate determination in the nucleus. Bugai, A., Hohmann, U., Lorenzo, A. et al. Nature (2026) 655:1070-1078. DOI 10.1038/s41586-026-10650-0 · 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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