9S83: JUBO4

Crystal structure of de novo designed binder JUBO4 and the LEDGF PWWP domain. Determined by X-ray diffraction at 2.1 Å resolution. Released 5 Aug 2026.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 1,408
Mol. weight: 18.5 kDa
Released: 5 Aug 2026

Explore 9S83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S83 contains 11 α-helices and 8 β-strands across 2 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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	20-26	7	1
α-helix	31	1
β-strand	32-38	7	1
α-helix	40-42	3
α-helix	45-58	14
α-helix	59-61	3
β-strand	65-69	5	1

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
β-strand	21-25	5	1
α-helix	27-29	3
α-helix	32-36	5
β-strand	40-44	5	1
β-strand	50-53	4	1
α-helix	55-57	3
β-strand	58-60	3	1
α-helix	62-64	3
α-helix	65-68	4
α-helix	77-86	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JUBO4	A	protein	74	synthetic construct
PC4 and SFRS1-interacting protein	B	protein	91	Homo sapiens	O75475 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9S83_1 JUBO4 (chains A)
GLAEKAKELAEKALAELGIEATVEVEEDEDGTLEITITIKPEQWSRENMYRAALAAGTAS
DEIADVNVRARPAE

Sequence of entity 2 (B), FASTA

>9S83_2 PC4 and SFRS1-interacting protein (chains B)
GMTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIF
PYSENKEKYGKPNKRKGFNEGLWEIDNNPKV

Primary citation

De novo design of proteinaceous binders targeting the LEDGF PWWP domain. Vantieghem, T., Delepine, J., Noppen, S. et al. Protein Sci (2026) 35:e70726-e70726. DOI 10.1002/pro.70726 · PubMed

Other PDB entries of the same protein (UniProt O75475 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRJ 1.3 Å, LEDGF/p75 IBD dimer
9S81 1.63 Å, Crystal structure of the LEDGF PWWP domain
5N88 1.7 Å, Crystal structure of antibody bound to viral protein
2B4J 2.02 Å, Structural basis for the recognition between HIV-1 integrase and LEDGF/p75
5OYM 2.05 Å, HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor
4FU6 2.1 Å, Crystal structure of the PSIP1 PWWP domain
3HPH 2.64 Å, Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
8PEO 2.69 Å, H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex
9S28 2.8 Å, MVV STC intasome in complex with LEDGF
9S29 2.8 Å, MVV CSC intasome in complex with LEDGF
3U88 3.0 Å, Crystal structure of human menin in complex with MLL1 and LEDGF
7OUF 3.0 Å, Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450

Browse structure collections

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