3EGH: PDB entry 3EGH

Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Mar 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Rattus norvegicus, Nodularia spumigena
Chains: 6
Atoms: 6,990
Mol. weight: 114.12 kDa
Ligands: MN
Released: 23 Mar 2010

Explore 3EGH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EGH contains 40 α-helices and 47 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
α-helix	18-21	4
α-helix	23	1
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	169-172	4	1
α-helix	184-187	4
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	229-238	10
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
α-helix	278-279	2
β-strand	280-285	6	2
β-strand	290-298	9	2

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
α-helix	18-21	4
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	121-123	3
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	229-238	10
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
α-helix	278-279	2
β-strand	280-285	6	6
β-strand	290-298	9	6

Chain C: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	431-434	4	2
α-helix	437-439	3
β-strand	450-451	2	2
α-helix	455	1
β-strand	456-461	6	2
α-helix	476-489	14
β-strand	493-500	8	9
β-strand	502	1	10
β-strand	505	1	10
β-strand	508-514	7	9
β-strand	524-531	8	9
α-helix	536-540	5
β-strand	548-552	5	9
β-strand	555-556	2	9
β-strand	560	1	9
α-helix	562-570	9
β-strand	575-582	8	9

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	431-434	4	6
α-helix	437-440	4
β-strand	450-451	2	6
α-helix	455	1
β-strand	456-461	6	6
α-helix	476-486	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	A, B	protein	329	Homo sapiens	P62136 (AlphaFold model)
Spinophilin	C, D	protein	170	Rattus norvegicus	O35274 (AlphaFold model)
nodularin R	E, F	protein	5	Nodularia spumigena

Sequence of entity 1 (A, B), FASTA

>3EGH_1 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (chains A, B)
GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKI
CGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLL
RGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQ
SMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDL
DLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADK
NKGKYGQFSGLNPGGRPITPPRNSAKAKK

Sequence of entity 2 (C, D), FASTA

>3EGH_2 Spinophilin (chains C, D)
GSMDEEDGEPPYEPESGCVEIPGLSEEEDPAPSRKIHFSTAPIQVFSTYSNEDYDRRNED
VDPMAASAEYELEKRVERLELFPVELEKDSEGLGISIIGMGAGADMGLEKLGIFVKTVTE
GGAAHRDGRIQVNDLLVEVDGTSLVGVTQSFAASVLRNTKGRVRFMIGRE

Sequence of entity 3 (E, F), FASTA

>3EGH_3 nodularin R (chains E, F)
DRXEX

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4

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

Primary citation

Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites. Ragusa, M.J., Dancheck, B., Critton, D.A. et al. Nat Struct Mol Biol (2010) 17:459-464. DOI 10.1038/nsmb.1786 · PubMed

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

6ZEG 1.09 Å, Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to…
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

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