8Z5M: PDB entry 8Z5M

human phosphorylase kinase alpha/gamma/delta subcomplex - inactive state. Determined by electron microscopy at 3.66 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.66 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,006
Mol. weight: 201.48 kDa
Released: 23 Apr 2025

Explore 8Z5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Z5M contains 79 α-helices and 46 β-strands across 3 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: 51 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	6-21	16
α-helix	23-25	3
β-strand	42-43	2	1
α-helix	44-49	6
α-helix	52-64	13
α-helix	68-93	26
α-helix	96-103	8
β-strand	115-116	2	1
α-helix	135-151	17
α-helix	160-172	13
α-helix	175-177	3
β-strand	180	1	2
β-strand	196	1	2
α-helix	199-211	13
β-strand	216	1	3
α-helix	219-221	3
β-strand	227	1	3
α-helix	233-244	12
α-helix	259-262	4
α-helix	273-287	15
β-strand	288	1	4
β-strand	293	1	4
α-helix	330-341	12
α-helix	346-357	12
β-strand	360-361	2	5
β-strand	367-368	2	5
β-strand	372-374	3	6
α-helix	375-376	2
α-helix	381-385	5
β-strand	393-395	3	6
α-helix	401-415	15
α-helix	420-423	4
β-strand	440-443	4	7
β-strand	445-446	2	8
α-helix	449-457	9
β-strand	463-464	2	8
β-strand	471-474	4	9
α-helix	476-482	7
α-helix	483-485	3
β-strand	488-489	2	10
β-strand	494-495	2	10
α-helix	498-499	2
α-helix	504-507	4
β-strand	510-512	3	9
β-strand	517-520	4	9
α-helix	523-525	3
α-helix	532-534	3
α-helix	536-552	17
β-strand	562-563	2	7
β-strand	566	1	8
α-helix	568-570	3
β-strand	571	1	11
β-strand	578	1	11
α-helix	580-589	10
α-helix	590-592	3
β-strand	594	1	12
β-strand	597	1	12
β-strand	599-601	3	7
α-helix	604-609	6
β-strand	613-615	3	9
α-helix	763-772	10
α-helix	776-789	14
β-strand	795	1	13
β-strand	805	1	13
α-helix	806-820	15
α-helix	826-833	8
α-helix	840-849	10
β-strand	853	1	14
α-helix	873-884	12
α-helix	885-887	3
α-helix	889-907	19
β-strand	917	1	14
α-helix	920-935	16
α-helix	939-947	9
α-helix	951-963	13
α-helix	1054-1064	11
α-helix	1071-1079	9
β-strand	1084-1087	4	15
β-strand	1090-1093	4	15
α-helix	1096-1099	4
α-helix	1105-1115	11
α-helix	1121-1140	20
β-strand	1148-1150	3	15
α-helix	1151-1169	19
α-helix	1186-1190	5
α-helix	1199-1213	15

Chain C: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
β-strand	20-28	9	16
β-strand	32-39	8	16
β-strand	45-52	8	16
α-helix	55-57	3
α-helix	61-81	21
β-strand	87	1	17
β-strand	90-95	6	16
β-strand	99-105	7	16
β-strand	111	1	17
α-helix	112-119	8
α-helix	124-143	20
β-strand	146-147	2	18
α-helix	153-155	3
β-strand	156-158	3	17
β-strand	164-166	3	17
β-strand	173-174	2	18
α-helix	188-190	3
α-helix	193-200	8
α-helix	209-212	4
α-helix	214-225	12
α-helix	235-244	10
α-helix	259-268	10
α-helix	277-278	2
α-helix	279-283	5
α-helix	286-288	3
α-helix	301-323	23
α-helix	330-335	6
α-helix	341-354	14
α-helix	367-369	3
α-helix	378-381	4

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	7-20	14
α-helix	30-40	11
α-helix	46-56	11
α-helix	66-73	8
α-helix	80-93	14
α-helix	103-113	11
α-helix	119-129	11
α-helix	139-145	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform	A	protein	1223	Homo sapiens	P46020 (AlphaFold model)
Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform	C	protein	387	Homo sapiens	Q16816 (AlphaFold model)
Calmodulin-3	D	protein	168	Homo sapiens	P0DP25 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Z5M_1 Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform (chains A)
MRSRSNSGVRLDGYARLVQQTILCHQNPVTGLLPASYDQKDAWVRDNVYSILAVWGLGLA
YRKNADRDEDKAKAYELEQSVVKLMRGLLHCMIRQVDKVESFKYSQSTKDSLHAKYNTKT
CATVVGDDQWGHLQLDATSVYLLFLAQMTASGLHIIHSLDEVNFIQNLVFYIEAAYKTAD
FGIWERGDKTNQGISELNASSVGMAKAALEALDELDLFGVKGGPQSVIHVLADEVQHCQS
ILNSLLPRASTSKEVDASLLSVVSFPAFAVEDSQLVELTKQEIITKLQGRYGCCRFLRDG
YKTPKEDPNRLYYEPAELKLFENIECEWPLFWTYFILDGVFSGNAEQVQEYKEALEAVLI
KGKNGVPLLPELYSVPPDRVDEEYQNPHTVDRVPMGKLPHMWGQSLYILGSLMAEGFLAP
GEIDPLNRRFSTVPKPDVVVQVSILAETEEIKTILKDKGIYVETIAEVYPIRVQPARILS
HIYSSLGCNNRMKLSGRPYRHMGVLGTSKLYDIRKTIFTFTPQFIDQQQFYLALDNKMIV
EMLRTDLSYLCSRWRMTGQPTITFPISHSMLDEDGTSLNSSILAALRKMQDGYFGGARVQ
TGKLSEFLTTSCCTHLSFMDPGPEGKLYSEDYDDNYDYLESGNWMNDYDSTSHARCGDEV
ARYLDHLLAHTAPHPKLAPTSQKGGLDRFQAAVQTTCDLMSLVTKAKELHVQNVHMYLPT
KLFQASRPSFNLLDSPHPRQENQVPSVRVEIHLPRDQSGEVDFKALVLQLKETSSLQEQA
DILYMLYTMKGPDWNTELYNERSATVRELLTELYGKVGEIRHWGLIRYISGILRKKVEAL
DEACTDLLSHQKHLTVGLPPEPREKTISAPLPYEALTQLIDEASEGDMSISILTQEIMVY
LAMYMRTQPGLFAEMFRLRIGLIIQVMATELAHSLRCSAEEATEGLMNLSPSAMKNLLHH
ILSGKEFGVERSVRPTDSNVSPAISIHEIGAVGATKTERTGIMQLKSEIKQVEFRRLSIS
AESQSPGTSMTPSSGSFPSAYDQQSSKDSRQGQWQRRRRLDGALNRVPVGFYQKVWKVLQ
KCHGLSVEGFVLPSSTTREMTPGEIKFSVHVESVLNRVPQPEYRQLLVEAILVLTMLADI
EIHSIGSIIAVEKIVHIANDLFLQEQKTLGADDTMLAKDPASGICTLLYDSAPSGRFGTM
TYLSKAAATYVQEFLPHSICAMQ

Sequence of entity 2 (C), FASTA

>8Z5M_2 Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform (chains C)
MTRDEALPDSHSAQDFYENYEPKEILGRGVSSVVRRCIHKPTSQEYAVKVIDVTGGGSFS
PEEVRELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKRGELFDYLTEKV
TLSEKETRKIMRALLEVICTLHKLNIVHRDLKPENILLDDNMNIKLTDFGFSCQLEPGER
LREVCGTPSYLAPEIIECSMNEDHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLR
MIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQNRYTAEEALAHPFFQQYLVEEVRHFS
PRGKFKVIALTVLASVRIYYQYRRVKPVTREIVIRDPYALRPLRRLIDAYAFRIYGHWVK
KGQQQNRAALFENTPKAVLLSLAEEDY

Sequence of entity 3 (D), FASTA

>8Z5M_3 Calmodulin-3 (chains D)
DYKDDDDKSGPDEVDASGRMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLG
QNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Primary citation

Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca 2. Ma, R., Du, B., Shi, C. et al. Nat Commun (2025) 16:3020-3020. DOI 10.1038/s41467-025-58363-8 · PubMed

Other PDB entries of the same protein (UniProt P46020 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XYA 2.7 Å, hPhK alpha-beta-gamma-delta subcomplex in inactive state
8JFK 2.9 Å, PhK holoenzyme in inactive state, muscle isoform
8JFL 2.9 Å, PhK holoenzyme in active state, muscle isoform
8XY7 2.9 Å, hPhK alpha-gamma subcomplex in active state
8XYB 3.1 Å, hPhK gamma-delta subcomplex in inactive state
8Z5P 3.41 Å, human phosphorylase kinase - inactive state
8Z5R 3.52 Å, human phosphorylase kinase alpha/gamma/delta subcomplex - phosphorylation and Ca2+ bound…
8Z5T 3.74 Å, human phosphorylase kinase - phosphorylation and Ca2+ bound state
8Z5Q 4.24 Å, human phosphorylase kinase - inactive state

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