8J2P: PML B-box2

Crystal structure of PML B-box2. Determined by X-ray diffraction at 2.09 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Escherichia coli (strain K12), Homo sapiens
Chains: 2
Atoms: 6,736
Mol. weight: 94.99 kDa
Ligands: ZN
Released: 20 Sept 2023

Explore 8J2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J2P contains 50 α-helices and 54 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: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	-183--180	4	10
α-helix	-173--159	15
β-strand	-155--152	4	10
α-helix	-147--139	9
β-strand	-131--127	5	10
α-helix	-126--124	3
α-helix	-123--118	6
β-strand	-114	1	11
α-helix	-113--111	3
α-helix	-107--104	4
β-strand	-101	1	12
α-helix	-99--94	6
β-strand	-92--91	2	13
β-strand	-88--87	2	13
β-strand	-84--79	6	10
β-strand	-76--72	5	14
β-strand	-62	1	15
α-helix	-61--59	3
α-helix	-58--50	9
β-strand	-45--43	3	14
α-helix	-36--27	10
β-strand	-23--19	5	16
β-strand	-15--8	8	16
α-helix	-4-10	15
α-helix	20-28	9
β-strand	32-37	6	14
α-helix	39-41	3
α-helix	42-46	5
β-strand	52-55	4	14
α-helix	56-58	3
β-strand	59-60	2	15
β-strand	63-64	2	15
α-helix	67	1
β-strand	68-69	2	17
β-strand	70-76	7	10
β-strand	77	1	11
α-helix	83-89	7
α-helix	90-94	5
α-helix	97-106	10
β-strand	111-112	2	10
β-strand	114	1	12
α-helix	115-121	7
α-helix	125-136	12
β-strand	138-139	2	17
α-helix	140-141	2
α-helix	146-161	16
α-helix	167-181	15
β-strand	187-188	2	18
β-strand	199-200	2	18
β-strand	202-204	3	16
β-strand	210-211	2	16
α-helix	213-218	6

Chain E: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	-184--180	5	1
α-helix	-173--159	15
β-strand	-156--152	5	1
α-helix	-147--139	9
β-strand	-131--127	5	1
α-helix	-126--124	3
α-helix	-123--118	6
β-strand	-114	1	2
α-helix	-113--111	3
α-helix	-107--104	4
β-strand	-101	1	3
α-helix	-99--94	6
β-strand	-92--91	2	4
β-strand	-88--87	2	4
β-strand	-84--79	6	1
β-strand	-76--72	5	5
β-strand	-62	1	6
α-helix	-61--59	3
α-helix	-58--50	9
β-strand	-45--43	3	5
α-helix	-36--27	10
β-strand	-23--18	6	7
β-strand	-15--8	8	7
α-helix	-4-10	15
α-helix	20-28	9
β-strand	32-37	6	5
α-helix	39-41	3
α-helix	42-46	5
β-strand	52-55	4	5
α-helix	56-58	3
β-strand	59-60	2	6
β-strand	63-64	2	6
α-helix	67	1
β-strand	68-69	2	8
β-strand	70-76	7	1
β-strand	77	1	2
α-helix	83-89	7
α-helix	90-94	5
α-helix	97-106	10
β-strand	111-112	2	1
β-strand	114	1	3
α-helix	115-121	7
α-helix	125-136	12
β-strand	138-139	2	8
α-helix	140-141	2
α-helix	146-161	16
α-helix	167-181	15
β-strand	187-188	2	9
β-strand	199-200	2	9
β-strand	202-204	3	7
β-strand	210-211	2	7
α-helix	213-218	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Protein PML	A, E	protein	428	Escherichia coli (strain K12), Homo sapiens	P0AEX9 (AlphaFold model), P29590 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8J2P_1 Maltose/maltodextrin-binding periplasmic protein,Protein PML (chains A, E)
MGKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPD
IIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYN
KDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDI
KDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTS
KVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKP
LGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVD
EALKDAQTNAAAEFKTNNIFCSNPNHRTPTLTSIYCRGCSKPLCCSCALLDSSHSELKCD
ISAEIQQR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural Basis of PML-RARA Oncoprotein Targeting by Arsenic Unravels a Cysteine Rheostat Controlling PML Body Assembly and Function. Bercier, P., Wang, Q.Q., Zang, N. et al. Cancer Discov (2023) 13:2548-2565. DOI 10.1158/2159-8290.CD-23-0453 · 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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