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- EMDB-39781: human phosphorylase kinase - phosphorylation and Ca2+ bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-39781
Titlehuman phosphorylase kinase - phosphorylation and Ca2+ bound state
Map dataEM map
Sample
  • Complex: human phosphorylase kinase - phosphorylation and Ca2+ bound state
    • Protein or peptide: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform
    • Protein or peptide: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
    • Protein or peptide: Calmodulin-3
  • Protein or peptide: Phosphorylase b kinase regulatory subunit beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsKinase / glycogenolysis / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / transporter inhibitor activity / positive regulation of glycogen catabolic process / tau-protein kinase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of high voltage-gated calcium channel activity / response to corticosterone ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / transporter inhibitor activity / positive regulation of glycogen catabolic process / tau-protein kinase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / presynaptic endocytosis / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / adenylate cyclase binding / protein phosphatase activator activity / catalytic complex / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol 3-kinase binding / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / substantia nigra development / regulation of heart rate / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / generation of precursor metabolites and energy / spindle microtubule / calcium channel regulator activity / response to calcium ion / mitochondrial membrane / Schaffer collateral - CA1 synapse / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / calcium-dependent protein binding / synaptic vesicle membrane / myelin sheath / growth cone / vesicle / carbohydrate metabolic process / transmembrane transporter binding / calmodulin binding / non-specific serine/threonine protein kinase / G protein-coupled receptor signaling pathway / protein domain specific binding / protein serine kinase activity / calcium ion binding / centrosome / protein kinase binding / enzyme binding / signal transduction / protein-containing complex / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphorylase kinase alpha/beta subunit / Phosphorylase b kinase regulatory subunit alpha/beta, C-terminal domain / Phosphorylase b kinase C-terminal domain / Phosphorylase kinase, gamma catalytic subunit / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / : / EF-hand domain pair ...Phosphorylase kinase alpha/beta subunit / Phosphorylase b kinase regulatory subunit alpha/beta, C-terminal domain / Phosphorylase b kinase C-terminal domain / Phosphorylase kinase, gamma catalytic subunit / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calmodulin-3 / Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform / Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform / Phosphorylase b kinase regulatory subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsMa R / Yan K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca.
Authors: Ruifang Ma / Bowen Du / Chen Shi / Lei Wang / Fuxing Zeng / Jie Han / Huiyi Guan / Yong Wang / Kaige Yan /
Abstract: Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage ...Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage Disease type IX (GSD IX), whereas the abnormal expression of PhK is also associated with tumors. Here, we use cryo-electron microscopy (cryo-EM) to resolve its near-atomic structures in the inactive and active states. These structures reveal the interactions and relative locations of the four subunits (αβγδ) within the PhK complex. Phosphorylated α and β subunits induce PhK to present a more compact state, while Ca causes sliding of the δ subunit along the helix of the γ subunit. Both actions synergistically activate PhK by enabling the de-inhibition of the γ subunit. We also identified different binding modes between PhK and its substrate, glycogen phosphorylase (GP), in two distinct states, using cross-linking mass spectrometry (XL-MS). This study provides valuable insights into the regulatory mechanisms of PhK, thereby enhancing our understanding of GSD IX and its implications in tumorigenesis.
History
DepositionApr 18, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39781.png

Downloads & links

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Map

FileDownload / File: emd_39781.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 525.6 Å		1.1 Å/pix.
x 480 pix.
= 525.6 Å		1.1 Å/pix.
x 480 pix.
= 525.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0845429 - 1.8283007
Average (Standard dev.)0.000016386668 (±0.052695923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 525.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39781_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_39781_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_39781_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

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Sample components

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Entire : human phosphorylase kinase - phosphorylation and Ca2+ bound state

EntireName: human phosphorylase kinase - phosphorylation and Ca2+ bound state
Components
  • Complex: human phosphorylase kinase - phosphorylation and Ca2+ bound state
    • Protein or peptide: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform
    • Protein or peptide: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
    • Protein or peptide: Calmodulin-3
  • Protein or peptide: Phosphorylase b kinase regulatory subunit beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: human phosphorylase kinase - phosphorylation and Ca2+ bound state

SupramoleculeName: human phosphorylase kinase - phosphorylation and Ca2+ bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle ...

MacromoleculeName: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.108688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLL HCMIRQVDKV E(SEP)FKY(SEP)Q(SEP)TK D(SEP)LHAKYNTK TCATVVGDDQ WGHLQLDATS VYLLF LAQM TASGLHIIHS ...String:
MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLL HCMIRQVDKV E(SEP)FKY(SEP)Q(SEP)TK D(SEP)LHAKYNTK TCATVVGDDQ WGHLQLDATS VYLLF LAQM TASGLHIIHS LDEVNFIQNL VFYIEAAYKT ADFGIWERGD KTNQGISELN AS(SEP)VGMAKAA LEALDELDLF GV KGGPQSV IHVLADEVQH CQ(SEP)ILNSLLP RASTSKEVDA SLLSVVSFPA FAVEDSQLVE LTKQEIITKL QGRYGCCRF LRDGYKTPKE DPNRLYYEPA ELKLFENIEC EWPLFWTYFI LDGVFSGNAE QVQEYKEALE AVLIKGKNGV PLLPELY (SEP)V PPDRVDEEYQ NPHTVDRVPM GKLPHMWGQS LYILGSLMAE GFLAPGEIDP LNRRFSTVPK PDVVVQVSIL AETE EIKTI LKDKGIYVET IAEVYPIRVQ PARIL(SEP)HIYS SLGCNNRMKL SGRPYRHMGV LGTSKLYDIR KTIFTFTPQF I DQQQFYLA LDNKMIVEML RTDL(SEP)YLCSR WRMTGQPTIT FPISHSMLDE DGTSLNSSIL AALRKMQDGY FGGARVQT G KLSEFLTTSC CTHLSFMDPG PEGKLY(SEP)EDY DDNYDYLESG NWMNDYDSTS HARCGDEVAR YLDHLLAH(TPO)A P HPKLAPTS QKGGLDRFQA AVQTTCDLM(SEP) LVTKAKELHV QNVHMYLPTK LFQA(SEP)RP(SEP)FN LLD(SEP)PH PRQ ENQVP(SEP)VRVE IHLPRDQ(SEP)GE VDFKALVLQL KETSSLQEQA DILYMLYTMK GPDWNTELYN ERSATVREL LTELYGKVGE IRHWGLIRYI SGILRKKVEA LDEACTDLLS HQKHL(TPO)VGLP PEPREKTISA PLPYEALTQL IDEASE GDM SISILTQEIM VYLAMYMRTQ PGLFAEMFRL RIGLIIQVMA TELAHSLRCS AEEATEGLMN LSPSAMKNLL HHIL (SEP)GKEF GVER(SEP)VRPTD SNV(SEP)PAI(SEP)IH EIGAVGA(TPO)KT ER(TPO)GIMQLK(SEP) EIKQVEF RR L(SEP)I(SEP)AE(SEP)Q(SEP)P GTSM(TPO)PSSGS FPSAYDQQSS KDSRQGQWQR RRRLDGALNR VPVGFYQK V WKVLQKCHGL SVEGFVLPSS TTREMTPGEI KFSVHVESVL NRVPQPEYRQ LLVEAILVLT MLADIEIHSI GSIIAVEKI VHIANDLFLQ EQKTLGADD(TPO) MLAKDPASGI CTLLYDSAP(SEP) GRFGTMTYLS KAAATYVQEF LPH(SEP)ICAM Q

UniProtKB: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform

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Macromolecule #2: Phosphorylase b kinase regulatory subunit beta

MacromoleculeName: Phosphorylase b kinase regulatory subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 126.152664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGAAGLTAE V(SEP)WKVLERRA RTKR(SEP)G(SEP)VYE PLK(SEP)INLPRP DNETLWDKLD HYYRIVKSTL LLYQ SPTTG LFPTKTCGGD QKAKIQDSLY CAAGAWALAL AYRRIDDDKG RTHELEHSAI KCMRGILYCY MRQADKVQQF KQDPR PTTC LHSVFNVHTG ...String:
MAGAAGLTAE V(SEP)WKVLERRA RTKR(SEP)G(SEP)VYE PLK(SEP)INLPRP DNETLWDKLD HYYRIVKSTL LLYQ SPTTG LFPTKTCGGD QKAKIQDSLY CAAGAWALAL AYRRIDDDKG RTHELEHSAI KCMRGILYCY MRQADKVQQF KQDPR PTTC LHSVFNVHTG DELLSYEEYG HLQINAVSLY LLYLVEMISS GLQIIYNTDE VSFIQNLVFC VERVYRVPDF GVWERG SKY NNGSTELHSS (SEP)VGLAKAALE AINGFNLFGN QGCSWSVIFV DLDAHNRNRQ (TPO)LC(SEP)LLPRES RSHNT DAAL LPCI(SEP)YPAFA LDDEVLFSQT LDKVVRKLKG KYGFKRFLRD GYRTSLEDPN RCYYKPAEIK LFDGIECEFP IF FLYMMID GVFRGNPKQV QEYQDLLTPV LHHTTEGYPV VPKYYYVPAD FVEYEKNNPG SQKRFPSNCG RDGKLFLWGQ ALY IIAKLL ADELISPKDI DPVQRYVPLK DQRNVSMRFS NQGPLENDLV VHVALIAESQ RLQVFLNTYG IQTQTPQQVE PIQI WPQQE LVKAYLQLGI NEKLGLSGRP DRPIGCLGTS KIYRILGKTV VCYPIIFDLS DFYMSQDVFL LIDDIKNALQ FIKQY WKMH GRPLFLVLIR EDNIRGSRFN PILDMLAALK KGIIGGVKVH VDRLQTLISG AVVEQLDFLR ISDTEELPEF K(SEP) FEELEPP KHSKVKRQ(SEP)(SEP) TPSAPELGQQ PDVNISEWKD KPTHEILQKL NDCSCLASQA ILLGILLKRE GPNFI TKEG TV(SEP)DHIERVY RRAGSQKLWL AVRYGAAFTQ KFSSSIAPHI TTFLVHGKQV TLGAFGHEEE VISNPLSPRV IQ NIIYYKC NTHDEREAVI QQELVIHIGW IISNNPELFS GMLKIRIGWI IHAMEYELQI RGGDKPALDL YQLSPSEVKQ LLL DILQPQ QNGRCWLNRR QIDGSLNRTP TGFYDRVWQI LERTPNGIIV AGKHLPQQPT LSDMTMYEMN FSLLVEDTLG NIDQ PQYRQ IVVELLMVVS IVLERNPELE FQDKVDLDRL VKEAFNEFQK DQSRLKEIEK QDDMT(SEP)FYNT PPLGKRG (TPO)C SYLTKAVMNL LLEGEVKPNN DDPCLIS

UniProtKB: Phosphorylase b kinase regulatory subunit beta

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Macromolecule #3: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/hea...

MacromoleculeName: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: phosphorylase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.084672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTRDEALPDS HSAQDFYENY EPKEILGRGV SSVVRRCIHK PTSQEYAVKV IDVTGGGSFS PEEVRELREA TLKEVDILRK VSGHPNIIQ LKDTYETNTF FFLVFDLMKR GELFDYLTEK VTLSEKETRK IMRALLEVIC TLHKLNIVHR DLKPENILLD D NMNIKLTD ...String:
MTRDEALPDS HSAQDFYENY EPKEILGRGV SSVVRRCIHK PTSQEYAVKV IDVTGGGSFS PEEVRELREA TLKEVDILRK VSGHPNIIQ LKDTYETNTF FFLVFDLMKR GELFDYLTEK VTLSEKETRK IMRALLEVIC TLHKLNIVHR DLKPENILLD D NMNIKLTD FGFSCQLEPG ERLREVCGTP SYLAPEIIEC SMNEDHPGYG KEVDMWSTGV IMYTLLAGSP PFWHRKQMLM LR MIMSGNY QFGSPEWDDY SDTVKDLVSR FLVVQPQNRY TAEEALAHPF FQQYLVEEVR HFSPRGKFKV IALTVLASVR IYY QYRRVK PVTREIVIRD PYALRPLRRL IDAYAFRIYG HWVKKGQQQN RAALFENTPK AVLLSLAEED Y

UniProtKB: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform

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Macromolecule #4: Calmodulin-3

MacromoleculeName: Calmodulin-3 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.921584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DYKDDDDKSG PDEVDASGRM ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFL TMMARKMKDT DSEEEIREAF RVFDKDGNGY ISAAELRHVM TNLGEKLTDE EVDEMIREAD IDGDGQVNYE E FVQMMTAK

UniProtKB: Calmodulin-3

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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