8DJI: Small ubiquitin-related modifier 1

Ternary complex of SUMO1 with the SIM of PML and zinc. Determined by X-ray diffraction at 1.97 Å resolution. Released 10 Aug 2022.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 797
Mol. weight: 14.22 kDa
Ligands: ZN
Released: 10 Aug 2022

Explore 8DJI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DJI contains 5 α-helices and 6 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	20-21	2
β-strand	22-27	6	1
β-strand	33-38	6	1
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	1
β-strand	69-70	2	1
α-helix	71-72	2
α-helix	77-80	4
β-strand	87-92	6	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11-13	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Small ubiquitin-related modifier 1	A	protein	97	Homo sapiens	P63165 (AlphaFold model)
Protein PML	B	protein	29	Homo sapiens	P29590 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DJI_1 Small ubiquitin-related modifier 1 (chains A)
GSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYAQRQGVPMN
SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

Sequence of entity 2 (B), FASTA

>8DJI_2 Protein PML (chains B)
GSGAGEAEERVVVISSSEDSDAENSSSRY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1. Lussier-Price, M., Wahba, H.M., Mascle, X.H. et al. Nucleic Acids Res (2022) 50:8331-8348. DOI 10.1093/nar/gkac620 · PubMed

Other PDB entries of the same protein (UniProt P63165 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UYR 1.3 Å, Crystal structure of K46-acetylated SUMO1 in complex with PML-SIM
4WJQ 1.35 Å, Crystal Structure of SUMO1 in complex with Daxx
6V7Q 1.35 Å, Crystal structure of SUMO1 in complex with phosphorylated PIAS-SIM2
6V7P 1.4 Å, Crystal structure of SUMO1 in complex with PIAS-SIM2
2UYZ 1.4 Å, Non-covalent complex between Ubc9 and SUMO1
6UYZ 1.4 Å, Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated DAXX
6UYV 1.4 Å, Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated PML-SIM
6UYP 1.42 Å, Crystal structure of K39-acetylated SUMO1 in complex with PML-SIM
4WJO 1.46 Å, Crystal Structure of SUMO1 in complex with PML
6V7S 1.47 Å, Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PIAS-SIM2
4WJN 1.5 Å, Crystal structure of SUMO1 in complex with phosphorylated PML
6UYQ 1.5 Å, Crystal structure of K45-acetylated SUMO1 in complex with PML-SIM

Browse structure collections

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