28XA: Human UAP56 NTD - LENG8-PCID2-SEM1 complex

Cryo-EM structure of the human UAP56 NTD - LENG8-PCID2-SEM1 complex. Determined by electron microscopy at 4.86 Å resolution. Released 24 Jun 2026.

Method: Electron microscopy
Resolution: 4.86 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 4
Atoms: 3,259
Mol. weight: 186.01 kDa
Released: 24 Jun 2026

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

Secondary structure: helices and β-sheets

28XA contains 41 α-helices and 7 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	577-592	16
α-helix	596-613	18
α-helix	618-633	16
α-helix	637-652	16
α-helix	659-673	15
α-helix	676-685	10
α-helix	688-692	5
α-helix	694-708	15
α-helix	711-719	9
α-helix	725-747	23
β-strand	752-753	2	1
α-helix	754-760	7
α-helix	765-773	9
β-strand	787-788	2	1
α-helix	790-793	4

Chain B: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-18	9
α-helix	22-29	8
α-helix	49-53	5
α-helix	55	1
α-helix	58-73	16
α-helix	77-97	21
α-helix	105-129	25
α-helix	136-153	18
α-helix	160-162	3
α-helix	164-167	4
α-helix	168-181	14
α-helix	185-187	3
α-helix	188-197	10
α-helix	206-222	17
α-helix	226-238	13
α-helix	245-261	17
β-strand	265-266	2	2
α-helix	267	1
α-helix	268-273	6
α-helix	277-286	10
α-helix	291-300	10
α-helix	302-307	6
α-helix	310-315	6
α-helix	317-333	17
β-strand	337-339	3	3
α-helix	340-349	10
α-helix	357-369	13
β-strand	375-378	4	3
β-strand	383-386	4	3

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-40	2	2
α-helix	51-62	12

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Leukocyte receptor cluster member 8	A	protein	688	Escherichia coli, Homo sapiens	P0AEX9 (AlphaFold model), Q96PV6 (AlphaFold model)
PCI domain-containing protein 2	B	protein	457	Homo sapiens	Q5JVF3 (AlphaFold model)
26S proteasome complex subunit SEM1	C	protein	70	Homo sapiens	P60896 (AlphaFold model)
Spliceosome RNA helicase DDX39B	H	protein	428	Homo sapiens	Q13838

Sequence of entity 1 (A), FASTA

>28XA_1 Maltose/maltodextrin-binding periplasmic protein,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

>28XA_2 PCI domain-containing protein 2 (chains B)
MGKPIPNPLLGLDSTGSGKPIPNPLLGLDSTGSGKPIPNPLLGLDSTSSGLEVLFQGPMA
HITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDEMF
AAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFANNA
DQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYFKI
NKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHR
SSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHE
AFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQC
ILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Sequence of entity 3 (C), FASTA

>28XA_3 26S proteasome complex subunit SEM1 (chains C)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Sequence of entity 4 (H), FASTA

>28XA_4 Spliceosome RNA helicase DDX39B (chains H)
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAI
VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC
HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALA
RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCR
KFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRC
IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF
NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI
SSYIEQTR

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 P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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