5J28: PDB entry 5J28

Ki67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Oct 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,393
Mol. weight: 80.69 kDa
Ligands: MLI
Released: 5 Oct 2016

Explore 5J28 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J28 contains 28 α-helices and 42 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: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	17-21	5
α-helix	32-48	17
β-strand	52-55	4	1
β-strand	59-62	4	2
β-strand	64	1	3
α-helix	69-79	11
β-strand	87-89	3	2
α-helix	100-113	14
β-strand	118-120	3	2
α-helix	128-131	4
α-helix	136-143	8
α-helix	146-156	11
β-strand	162-165	4	1
β-strand	169-172	4	1
α-helix	184-187	4
α-helix	200-206	7
β-strand	208-209	2	4
β-strand	213	1	5
β-strand	216-218	3	4
β-strand	225-227	3	4
α-helix	229-239	11
β-strand	243-246	4	1
β-strand	255-258	4	1
β-strand	263-266	4	1
β-strand	267	1	3
α-helix	272-274	3
β-strand	276	1	6
β-strand	280-285	6	2
β-strand	290-298	9	2

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	17-21	5
α-helix	23	1
α-helix	32-48	17
β-strand	52-55	4	7
β-strand	59-62	4	8
β-strand	64	1	9
α-helix	69-79	11
β-strand	87-89	3	8
α-helix	100-113	14
β-strand	118-120	3	8
α-helix	128-131	4
α-helix	136-143	8
α-helix	146-156	11
β-strand	162-165	4	7
β-strand	169-172	4	7
α-helix	184-187	4
α-helix	200-206	7
β-strand	208-209	2	10
β-strand	213	1	6
β-strand	216-218	3	10
β-strand	225-227	3	10
α-helix	229-239	11
β-strand	243-246	4	7
β-strand	255-258	4	7
β-strand	263-266	4	7
β-strand	267	1	9
α-helix	272-274	3
β-strand	276	1	5
β-strand	280-285	6	8
β-strand	290-298	9	8

Chain C: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	507-508	2	2
α-helix	513-514	2
β-strand	515-517	3	2
β-strand	528	1	2
α-helix	529-533	5

Chain D: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	507-508	2	8
β-strand	515-517	3	8
β-strand	528	1	8
α-helix	529-533	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase PP1-gamma catalytic subunit	A, B	protein	305	Homo sapiens	P36873 (AlphaFold model)
Antigen KI-67	C, D	protein	46	Homo sapiens	P46013

Sequence of entity 1 (A, B), FASTA

>5J28_1 Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (chains A, B)
GHMLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICG
DIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRG
NHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSM
EQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDL
ICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKK
PNATR

Sequence of entity 2 (C, D), FASTA

>5J28_2 Antigen KI-67 (chains C, D)
GAMGYSEGIPLKRRRVSFGGHLRPELFDENLPPNMPLKRGEAPTKR

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	2

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

Primary citation

The Ki-67 and RepoMan mitotic phosphatases assemble via an identical, yet novel mechanism. Kumar, G.S., Gokhan, E., De Munter, S. et al. Elife (2016) 5. DOI 10.7554/eLife.16539 · PubMed

Other PDB entries of the same protein (UniProt P36873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5INB 1.3 Å, RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex
1JK7 1.9 Å, Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1
4UT2 1.96 Å, X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate
1IT6 2.0 Å, Crystal structure of the complex between calyculin a and the catalytic subunit of…
1U32 2.0 Å, Crystal structure of a Protein Phosphatase-1: Calcineurin Hybrid Bound to Okadaic Acid
2BCD 2.1 Å, X-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound
4UT3 2.19 Å, X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide
2BDX 2.3 Å, X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1
7SD0 2.95 Å, Cryo-EM structure of the SHOC2:PP1C:MRAS complex
8B5R 6.1 Å, p97-p37-SPI substrate complex

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