9RV1: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

Cryo-EM structure of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex. Determined by electron microscopy at 2.62 Å resolution. Released 24 Jun 2026.

Method
Electron microscopy
Resolution
2.62 Å
Organism
Homo sapiens
Chains
5
Atoms
8,832
Mol. weight
152.13 kDa
Ligands
ANP, MG
Released
24 Jun 2026

Explore 9RV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RV1 contains 63 α-helices and 30 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: 22 helices, 5 β-strands

ElementResiduesLengthSheet
α-helix52-554
α-helix63-719
β-strand8011
α-helix811
α-helix89-902
β-strand9111
α-helix921
α-helix98-1003
α-helix108-1114
α-helix116-1172
α-helix118-12710
α-helix128-1336
α-helix140-15920
α-helix165-18521
α-helix197-21721
α-helix225-23511
α-helix240-2478
α-helix251-2544
α-helix257-27014
α-helix274-28310
α-helix286-31126
β-strand317-32042
α-helix322-3276
α-helix333-34210
α-helix345-3462
β-strand34712
β-strand352-35542
Chain B: 20 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix7-1913
α-helix22-287
α-helix57-6711
α-helix78-9720
α-helix105-12521
α-helix136-15419
α-helix167-18115
α-helix185-1873
α-helix188-19710
α-helix206-22217
α-helix226-23813
β-strand24113
α-helix245-26117
β-strand265-26624
α-helix2671
α-helix268-2736
α-helix278-28811
α-helix291-30010
α-helix302-3076
α-helix311-33222
β-strand337-33935
α-helix340-34910
α-helix357-37014
β-strand375-37845
β-strand383-38645
Chain C: 3 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix20-223
α-helix29-313
β-strand3213
β-strand39-4024
α-helix51-6212
Chain H: 18 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix11-133
α-helix39-424
α-helix46-483
α-helix54-629
α-helix70-8011
β-strand85-8846
α-helix95-10612
β-strand11017
β-strand11317
β-strand116-11946
α-helix123-13614
β-strand145-14846
α-helix154-1629
β-strand168-17146
α-helix173-1819
β-strand192-19656
α-helix198-2036
α-helix205-21713
β-strand223-22866
α-helix236-2405
β-strand247-24936
β-strand262-26878
α-helix273-28412
β-strand289-29358
α-helix297-30913
β-strand314-31748
β-strand31919
β-strand32119
α-helix323-33412
β-strand340-34348
β-strand356-36168
α-helix368-3758
β-strand385-39178
α-helix394-40613
β-strand412-41328
α-helix414-4152

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA (5'-r(p*up*up*up*up*up*up*up*up*up*up*up*up*up*up*u)-3')1RNA15Homo sapiens
SAC3 domain-containing protein 1Aprotein404Homo sapiensA6NKF1 (AlphaFold model)
PCI domain-containing protein 2Bprotein399Homo sapiensQ5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1Cprotein70Homo sapiensP60896 (AlphaFold model)
Spliceosome RNA helicase DDX39BHprotein428Homo sapiensQ13838 (AlphaFold model)
Sequence of entity 1 (1), FASTA
>9RV1_1 RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') (chains 1)
UUUUUUUUUUUUUUU
Sequence of entity 2 (A), FASTA
>9RV1_2 SAC3 domain-containing protein 1 (chains A)
MAGRRAQTGSAPPRPAAPHPRPASRAFPQHCRPRDAERPPSPRSPLMPGCELPVGTCPDM
CPAAERAQREREHRLHRLEVVPGCRQDPPRADPQRAVKEYSRPAAGKPRPPPSQLRPPSV
LLATVRYLAGEVAESADIARAEVASFVADRLRAVLLDLALQGAGDAEAAVVLEAALATLL
TVVARLGPDAARGPADPVLLQAQVQEGFGSLRRCYARGAGPHPRQPAFQGLFLLYNLGSV
EALHEVLQLPAALRACPPLRKALAVDAAFREGNAARLFRLLQTLPYLPSCAVQCHVGHAR
REALARFARAFSTPKGQTLPLGFMVNLLALDGLREARDLCQAHGLPLDGEERVVFLRGRY
VEEGLPPASTCKVLVESKLRGRTLEEVVMAEEEDEGTDRPGSPA
Sequence of entity 3 (B), FASTA
>9RV1_3 PCI domain-containing protein 2 (chains B)
MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDE
MFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFAN
NADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYF
KINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHC
HRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAK
HEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEV
QCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC
Sequence of entity 4 (C), FASTA
>9RV1_4 26S proteasome complex subunit SEM1 (chains C)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 5 (H), FASTA
>9RV1_5 Spliceosome RNA helicase DDX39B (chains H)
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAI
VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC
HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALA
RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR
KFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRC
IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF
NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI
SSYIEQTR

Ligands and cofactors

IDNameFormulaCopies
ANPPhosphoaminophosphonic acid-adenylate esterC10 H17 N6 O12 P31
MGMagnesium ionMg1

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 A6NKF1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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