5YUF: PML RING tetramer

Crystal Structure of PML RING tetramer. Determined by X-ray diffraction at 1.6 Å resolution. Released 11 Apr 2018.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,635
Mol. weight: 22.99 kDa
Ligands: ZN
Released: 11 Apr 2018

Explore 5YUF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YUF contains 17 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	52-53	2
β-strand	54	1	1
β-strand	55-56	2	2
β-strand	63-64	2	2
β-strand	68	1	3
α-helix	78-82	5
β-strand	87	1	4
α-helix	93	1
β-strand	94	1	4
α-helix	95-96	2

Chain B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	3
β-strand	55-56	2	5
β-strand	63-64	2	5
α-helix	67	1
β-strand	68	1	1
α-helix	69-70	2
α-helix	78-82	5
β-strand	87	1	6
α-helix	93	1
β-strand	94	1	6
α-helix	95-96	2

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	7
β-strand	55-56	2	8
β-strand	63-64	2	8
β-strand	68	1	9
α-helix	78-82	5
β-strand	87	1	10
α-helix	93	1
β-strand	94	1	10
α-helix	95	1

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	9
β-strand	55-56	2	11
β-strand	63-64	2	11
α-helix	67	1
β-strand	68	1	7
α-helix	69-70	2
α-helix	78-82	5
β-strand	87	1	12
α-helix	93	1
β-strand	94	1	12
α-helix	95	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein PML	A, B, C, D	protein	51	Homo sapiens	P29590 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5YUF_1 Protein PML (chains A, B, C, D)
EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

RING tetramerization is required for nuclear body biogenesis and PML sumoylation. Wang, P., Benhenda, S., Wu, H. et al. Nat Commun (2018) 9:1277-1277. DOI 10.1038/s41467-018-03498-0 · PubMed

Other PDB entries of the same protein (UniProt P29590 (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
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
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
6UYS 1.59 Å, Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PML-SIM
6UYO 1.64 Å, Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM
6UYU 1.66 Å, Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM
6UYT 1.66 Å, Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated PML-SIM
8DJH 1.77 Å, Ternary complex of SUMO1 with a phosphomimetic SIM of PML and zinc
8DJI 1.97 Å, Ternary complex of SUMO1 with the SIM of PML and zinc

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