6IMQ: PML B1-box multimers

Crystal structure of PML B1-box multimers. Determined by X-ray diffraction at 2.06 Å resolution. Released 31 Jul 2019.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,700
Mol. weight: 24.33 kDa
Ligands: ZN
Released: 31 Jul 2019

Explore 6IMQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IMQ contains 10 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	121-124	4	1
β-strand	128	1	2
β-strand	135	1	2
α-helix	136	1
β-strand	138-140	3	3
β-strand	145-147	3	3
α-helix	149-158	10
β-strand	163-165	3	3

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	120-123	4	1
β-strand	128	1	4
β-strand	135	1	4
α-helix	136	1
β-strand	138-140	3	5
β-strand	145-147	3	5
α-helix	149-158	10
β-strand	163-165	3	5
α-helix	166-167	2

Chain C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	121-123	3	6
β-strand	128	1	7
β-strand	135	1	7
α-helix	136	1
β-strand	138-140	3	8
β-strand	145-147	3	8
α-helix	149-158	10
β-strand	163-165	3	8

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	121-123	3	6
α-helix	127	1
β-strand	128	1	9
α-helix	129	1
β-strand	135	1	9
β-strand	138-140	3	10
β-strand	145-147	3	10
α-helix	149-158	10
β-strand	163-165	3	10

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

>6IMQ_1 Protein PML (chains A, B, C, D)
GSRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (CL) are not listed.

Primary citation

B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis. Li, Y., Ma, X., Chen, Z. et al. Nat Commun (2019) 10:3789-3789. DOI 10.1038/s41467-019-11746-0 · 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
5YUF 1.6 Å, Crystal Structure of PML RING tetramer
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

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