8XYB: HPhK gamma-delta subcomplex in inactive state

hPhK gamma-delta subcomplex in inactive state. Determined by electron microscopy at 3.1 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,554
Mol. weight: 199.61 kDa
Ligands: FAR
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8XYB contains 41 α-helices and 24 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1053-1058	6
α-helix	1071-1079	9
β-strand	1084-1087	4	1
β-strand	1090-1093	4	1
α-helix	1095-1099	5
α-helix	1105-1115	11
α-helix	1121-1140	20
β-strand	1141	1	2
β-strand	1148-1150	3	1
α-helix	1151-1169	19
α-helix	1177	1
β-strand	1178	1	3
α-helix	1179	1
β-strand	1185	1	3
α-helix	1186-1190	5
β-strand	1194	1	4
α-helix	1199-1214	16
β-strand	1220	1	2

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	20-27	8	6
β-strand	32-39	8	6
β-strand	44-52	9	6
α-helix	55-57	3
α-helix	61-80	20
β-strand	87	1	7
β-strand	92-95	4	6
β-strand	99-105	7	6
β-strand	111	1	7
α-helix	112-118	7
α-helix	124-143	20
β-strand	147	1	8
α-helix	153-155	3
β-strand	156-158	3	7
β-strand	164-166	3	7
β-strand	173	1	8
α-helix	174-176	3
β-strand	181	1	9
α-helix	188-190	3
α-helix	193-200	8
β-strand	207	1	9
α-helix	211-225	15
α-helix	235-244	10
α-helix	253-255	3
α-helix	259-269	11
α-helix	273-275	3
α-helix	279-282	4
α-helix	286-288	3
α-helix	301-324	24
α-helix	325-328	4
α-helix	330-335	6
α-helix	341-354	14
α-helix	356-358	3
α-helix	367-370	4
β-strand	371	1	4
α-helix	376-379	4

Chain D: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28-29	2	5
α-helix	30-39	10
α-helix	46-57	12
β-strand	63-64	2	5
α-helix	66-73	8
α-helix	79-93	15
α-helix	103-113	11
α-helix	119-129	11
α-helix	139-147	9

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)
Calmodulin-1	D	protein	149	Homo sapiens	P0DP23 (AlphaFold model)
Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform	C	protein	387	Homo sapiens	Q16816 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8XYB_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 (D), FASTA

>8XYB_2 Calmodulin-1 (chains D)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 3 (C), FASTA

>8XYB_3 Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform (chains C)
MTRDEALPDSHSAQDFYENYEPKEILGRGVSSVVRRCIHKPTSQEYAVKVIDVTGGGSFS
PEEVRELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKRGELFDYLTEKV
TLSEKETRKIMRALLEVICTLHKLNIVHRDLKPENILLDDNMNIKLTDFGFSCQLEPGER
LREVCGTPSYLAPEIIECSMNEDHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLR
MIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQNRYTAEEALAHPFFQQYLVEEVRHFS
PRGKFKVIALTVLASVRIYYQYRRVKPVTREIVIRDPYALRPLRRLIDAYAFRIYGHWVK
KGQQQNRAALFENTPKAVLLSLAEEDY

Ligands and cofactors

ID	Name	Formula	Copies
FAR	Farnesyl	C15 H26	1

Primary citation

Architecture and activation of human muscle phosphorylase kinase. Yang, X., Zhu, M., Lu, X. et al. Nat Commun (2024) 15:2719-2719. DOI 10.1038/s41467-024-47049-2 · 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
8Z5P 3.41 Å, human phosphorylase kinase - inactive state
8Z5R 3.52 Å, human phosphorylase kinase alpha/gamma/delta subcomplex - phosphorylation and Ca2+ bound…
8Z5M 3.66 Å, human phosphorylase kinase alpha/gamma/delta subcomplex - inactive state
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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