8XYA: PDB entry 8XYA

hPhK alpha-beta-gamma-delta subcomplex in inactive state. Determined by electron microscopy at 2.7 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 20,357
Mol. weight: 324.85 kDa
Ligands: FAR
Released: 3 Apr 2024

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

Secondary structure: helices and β-sheets

8XYA contains 147 α-helices and 91 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: 59 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-18	13
α-helix	19-23	5
β-strand	41-43	3	1
α-helix	44-50	7
α-helix	52-62	11
α-helix	68-93	26
α-helix	96-104	9
α-helix	108-110	3
α-helix	112-113	2
β-strand	115-117	3	1
α-helix	135-150	16
α-helix	159-173	15
α-helix	174-177	4
β-strand	180	1	2
β-strand	196	1	2
α-helix	199-211	13
β-strand	215-216	2	3
α-helix	224-226	3
β-strand	227-228	2	3
α-helix	229	1
α-helix	232-245	14
β-strand	256	1	4
α-helix	257-259	3
α-helix	260-263	4
α-helix	273-286	14
β-strand	288	1	5
β-strand	293-294	2	5
β-strand	296	1	4
α-helix	315-321	7
β-strand	327-328	2	5
α-helix	330-342	13
α-helix	347-356	10
α-helix	359	1
β-strand	360-362	3	6
β-strand	366-368	3	6
β-strand	372-374	3	5
α-helix	377-379	3
α-helix	380-385	6
β-strand	393-395	3	5
α-helix	401-414	14
α-helix	420-423	4
α-helix	428-432	5
α-helix	436-438	3
β-strand	439-446	8	7
α-helix	449-457	9
β-strand	463-464	2	7
β-strand	472-474	3	8
α-helix	476-482	7
α-helix	483-485	3
β-strand	488-489	2	9
β-strand	494-495	2	9
α-helix	504-507	4
β-strand	510-513	4	8
β-strand	516-520	5	8
α-helix	523-525	3
α-helix	536-552	17
β-strand	561-566	6	7
α-helix	568-570	3
β-strand	571	1	10
β-strand	578	1	10
α-helix	580-590	11
β-strand	593-594	2	7
β-strand	597-601	5	7
β-strand	613-615	3	8
α-helix	617-619	3
α-helix	660-668	9
α-helix	780-788	9
α-helix	810-820	11
α-helix	823-833	11
α-helix	840-848	9
β-strand	853-856	4	11
β-strand	865-867	3	11
α-helix	873-882	10
α-helix	888-907	20
α-helix	909-912	4
β-strand	917-919	3	11
α-helix	920-933	14
α-helix	939-948	10
α-helix	951-963	13
α-helix	1053-1058	6
α-helix	1071-1079	9
β-strand	1084-1087	4	12
β-strand	1090-1093	4	12
α-helix	1095-1099	5
α-helix	1105-1115	11
α-helix	1121-1140	20
β-strand	1141	1	13
β-strand	1148-1150	3	12
α-helix	1151-1169	19
α-helix	1177	1
β-strand	1178	1	14
α-helix	1179	1
β-strand	1185	1	14
α-helix	1186-1190	5
β-strand	1194	1	15
α-helix	1199-1214	16
β-strand	1220	1	13

Chain B: 57 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
α-helix	56-60	5
α-helix	61-63	3
β-strand	81-83	3	16
α-helix	84-101	18
α-helix	110-130	21
α-helix	133-141	9
α-helix	149-150	2
β-strand	152-154	3	16
β-strand	160	1	16
α-helix	172-188	17
α-helix	196-210	15
α-helix	211-214	4
β-strand	217	1	17
β-strand	233	1	17
α-helix	236-249	14
β-strand	252-253	2	18
β-strand	264-265	2	18
α-helix	266	1
α-helix	269-282	14
α-helix	296-300	5
α-helix	310-324	15
β-strand	325	1	19
β-strand	330-331	2	19
α-helix	356-358	3
α-helix	362-363	2
β-strand	364-365	2	19
α-helix	367-379	13
α-helix	382-395	14
β-strand	397-398	2	20
β-strand	404-405	2	20
β-strand	410-411	2	19
α-helix	414-416	3
α-helix	417-422	6
β-strand	430-431	2	19
α-helix	442-455	14
β-strand	478	1	21
β-strand	483	1	21
α-helix	493-494	2
β-strand	495-501	7	22
α-helix	504-511	8
β-strand	518	1	22
β-strand	527-529	3	23
α-helix	531-538	8
β-strand	544	1	24
β-strand	549	1	24
α-helix	559-563	5
β-strand	565-568	4	23
β-strand	571-575	5	23
α-helix	576-577	2
α-helix	578-580	3
α-helix	591-608	18
α-helix	614-615	2
β-strand	616-621	6	22
α-helix	623-626	4
α-helix	628-630	3
α-helix	631-643	13
β-strand	645-646	2	25
β-strand	649-650	2	25
β-strand	651-653	3	22
α-helix	658-660	3
β-strand	665-667	3	23
α-helix	670-673	4
α-helix	716-720	5
α-helix	727-733	7
α-helix	737-750	14
β-strand	756	1	26
β-strand	761	1	26
α-helix	762-776	15
α-helix	779-787	9
α-helix	796-804	9
β-strand	809-812	4	27
β-strand	820-822	3	27
α-helix	828-833	6
α-helix	834-838	5
α-helix	845-863	19
α-helix	865-868	4
β-strand	873-875	3	27
α-helix	876-891	16
α-helix	896-898	3
α-helix	904-913	10
α-helix	924-933	10
α-helix	941-949	9
β-strand	956-958	3	28
β-strand	961-963	3	28
α-helix	968-971	4
α-helix	977-987	11
α-helix	993-1012	20
β-strand	1022-1023	2	28
α-helix	1024-1042	19
α-helix	1052-1056	5
α-helix	1065-1077	13
α-helix	1081-1085	5

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	20-27	8	30
β-strand	32-39	8	30
β-strand	44-52	9	30
α-helix	55-57	3
α-helix	61-80	20
β-strand	87	1	31
β-strand	92-95	4	30
β-strand	99-105	7	30
β-strand	111	1	31
α-helix	112-118	7
α-helix	124-143	20
β-strand	147	1	32
α-helix	153-155	3
β-strand	156-158	3	31
β-strand	164-166	3	31
β-strand	173	1	32
α-helix	174-176	3
β-strand	181	1	33
α-helix	188-190	3
α-helix	193-200	8
β-strand	207	1	33
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	15
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	29
α-helix	30-39	10
α-helix	46-57	12
β-strand	63-64	2	29
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)
Phosphorylase b kinase regulatory subunit beta	B	protein	1093	Homo sapiens	Q93100 (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

>8XYA_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 (B), FASTA

>8XYA_2 Phosphorylase b kinase regulatory subunit beta (chains B)
MAGAAGLTAEVSWKVLERRARTKRSGSVYEPLKSINLPRPDNETLWDKLDHYYRIVKSTL
LLYQSPTTGLFPTKTCGGDQKAKIQDSLYCAAGAWALALAYRRIDDDKGRTHELEHSAIK
CMRGILYCYMRQADKVQQFKQDPRPTTCLHSVFNVHTGDELLSYEEYGHLQINAVSLYLL
YLVEMISSGLQIIYNTDEVSFIQNLVFCVERVYRVPDFGVWERGSKYNNGSTELHSSSVG
LAKAALEAINGFNLFGNQGCSWSVIFVDLDAHNRNRQTLCSLLPRESRSHNTDAALLPCI
SYPAFALDDEVLFSQTLDKVVRKLKGKYGFKRFLRDGYRTSLEDPNRCYYKPAEIKLFDG
IECEFPIFFLYMMIDGVFRGNPKQVQEYQDLLTPVLHHTTEGYPVVPKYYYVPADFVEYE
KNNPGSQKRFPSNCGRDGKLFLWGQALYIIAKLLADELISPKDIDPVQRYVPLKDQRNVS
MRFSNQGPLENDLVVHVALIAESQRLQVFLNTYGIQTQTPQQVEPIQIWPQQELVKAYLQ
LGINEKLGLSGRPDRPIGCLGTSKIYRILGKTVVCYPIIFDLSDFYMSQDVFLLIDDIKN
ALQFIKQYWKMHGRPLFLVLIREDNIRGSRFNPILDMLAALKKGIIGGVKVHVDRLQTLI
SGAVVEQLDFLRISDTEELPEFKSFEELEPPKHSKVKRQSSTPSAPELGQQPDVNISEWK
DKPTHEILQKLNDCSCLASQAILLGILLKREGPNFITKEGTVSDHIERVYRRAGSQKLWL
AVRYGAAFTQKFSSSIAPHITTFLVHGKQVTLGAFGHEEEVISNPLSPRVIQNIIYYKCN
THDEREAVIQQELVIHIGWIISNNPELFSGMLKIRIGWIIHAMEYELQIRGGDKPALDLY
QLSPSEVKQLLLDILQPQQNGRCWLNRRQIDGSLNRTPTGFYDRVWQILERTPNGIIVAG
KHLPQQPTLSDMTMYEMNFSLLVEDTLGNIDQPQYRQIVVELLMVVSIVLERNPELEFQD
KVDLDRLVKEAFNEFQKDQSRLKEIEKQDDMTSFYNTPPLGKRGTCSYLTKAVMNLLLEG
EVKPNNDDPCLIS

Sequence of entity 3 (D), FASTA

>8XYA_3 Calmodulin-1 (chains D)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 4 (C), FASTA

>8XYA_4 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	2

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:

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…
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

Browse structure collections

About this viewer

MolViewer shows 8XYA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.