6ZEG: PDB entry 6ZEG

Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580). Determined by X-ray diffraction at 1.09 Å resolution. Released 30 Sept 2020.

Method: X-ray diffraction
Resolution: 1.09 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,225
Mol. weight: 92.76 kDa
Ligands: 16P, PO4, MN
Released: 30 Sept 2020

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

Secondary structure: helices and β-sheets

6ZEG contains 38 α-helices and 36 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: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	19-21	3
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	121-123	3
α-helix	128-131	4
α-helix	136-143	8
α-helix	146-156	11
β-strand	162-165	4	1
β-strand	169-171	3	1
α-helix	183-187	5
α-helix	194-196	3
α-helix	200-206	7
β-strand	208-209	2	4
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	280-285	6	2
β-strand	290-297	8	2
α-helix	324-326	3

Chain B: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	2
α-helix	9-18	10
α-helix	23	1
α-helix	32-48	17
β-strand	52-55	4	5
β-strand	59-62	4	6
β-strand	64	1	7
α-helix	69-79	11
β-strand	87-89	3	6
α-helix	100-113	14
β-strand	118-120	3	6
α-helix	128-131	4
α-helix	136-143	8
α-helix	146-156	11
β-strand	162-165	4	5
β-strand	169-171	3	5
α-helix	184-187	4
α-helix	194-196	3
α-helix	200-206	7
β-strand	208-209	2	8
β-strand	216-218	3	8
β-strand	225-227	3	8
α-helix	229-239	11
β-strand	243-246	4	5
β-strand	255-258	4	5
β-strand	263-266	4	5
β-strand	267	1	7
α-helix	272-274	3
β-strand	280-285	6	6
β-strand	290-297	8	6
α-helix	329-330	2

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	516-518	3
β-strand	521-522	2	2
β-strand	527-530	4	2
α-helix	531-532	2
α-helix	541-543	3
α-helix	547-563	17
α-helix	569-574	6

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	521-530	10	6
α-helix	531-532	2
α-helix	541-544	4
α-helix	547-563	17
α-helix	569-574	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis…	A, B	protein	338	Homo sapiens	P62136 (AlphaFold model), Q9UQB8 (AlphaFold model)
Phosphatase and actin regulator	C, D	protein	70	Homo sapiens	Q9C0D0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ZEG_1 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2 (chains A, B)
GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKI
CGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLL
RGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQ
SMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDL
DLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADK
NKGSGSGSGSGSGSGSGSGSGQQGKSSSTGNLLDKDDL

Sequence of entity 2 (C, D), FASTA

>6ZEG_2 Phosphatase and actin regulator (chains C, D)
GPLGSRKILIRFSDYVEVADAQDYDRRADKPWTRLTAADKAAIRKELNEFKSTEMEVHEL
SRHLTRFHRP

Ligands and cofactors

ID	Name	Formula	Copies
16P	3,6,9,12,15,18-hexaoxaicosane	C14 H30 O6	1
PO4	Phosphate ion	O4 P	2
MN	Manganese (II) ion	Mn	4

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

Primary citation

Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme. Fedoryshchak, R.O., Prechova, M., Butler, A. et al. Elife (2020) 9. DOI 10.7554/eLife.61509 · PubMed

Other PDB entries of the same protein (UniProt P62136 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZEH 1.3 Å, Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha…
6ZEI 1.39 Å, Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)]…
6DNO 1.45 Å, Crystal structure of Protein Phosphatase 1 (PP1) bound to the muscle glycogen-targeting…
4MOV 1.45 Å, 1.45 A Resolution Crystal Structure of Protein Phosphatase 1
6OBR 1.5 Å, PP1 Y134A in complex with Microcystin LR
3E7A 1.63 Å, Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R
3E7B 1.7 Å, Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin inhibitor Tautomycin
8SW6 1.76 Å, Protein Phosphatase 1 in complex with PP1-specific Phosphatase targeting peptide…
6ZEJ 1.78 Å, Structure of PP1-Phactr1 chimera [PP1(7-304) + linker (SGSGS) + Phactr1(526-580)]
7T0Y 1.8 Å, The Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme
6OBS 1.8 Å, PP1 Y134K
6OBQ 1.84 Å, PP1 H66K in complex with Microcystin LR

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