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- EMDB-39777: human phosphorylase kinase - inactive state -

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Basic information

Entry
Database: EMDB / ID: EMD-39777
Titlehuman phosphorylase kinase - inactive state
Map dataEM map
Sample
  • Complex: human phosphorylase kinase - inactive state
    • Protein or peptide: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform
    • Protein or peptide: Phosphorylase b kinase regulatory subunit beta
    • Protein or peptide: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
    • Protein or peptide: Calmodulin-3
KeywordsKinase / glycogenolysis / SIGNALING PROTEIN / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / tau-protein kinase / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / glycogen metabolic process / presynaptic endocytosis ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / tau-protein kinase / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / glycogen metabolic process / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / generation of precursor metabolites and energy / spindle microtubule / long-term synaptic potentiation / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / vesicle / transmembrane transporter binding / carbohydrate metabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / G protein-coupled receptor signaling pathway / protein serine kinase activity / centrosome / calcium ion binding / 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: 3.41 Å
AuthorsMa R / Yan K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271251 China
CitationJournal: To Be Published
Title: Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca2+
Authors: Ma R / Yan K
History
DepositionApr 18, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39777.png

Downloads & links

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Map

FileDownload / File: emd_39777.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.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.16
Minimum - Maximum-1.8137527 - 2.6103024
Average (Standard dev.)-0.0008009811 (±0.041845914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39777_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_39777_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_39777_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human phosphorylase kinase - inactive state

EntireName: human phosphorylase kinase - inactive state
Components
  • Complex: human phosphorylase kinase - inactive state
    • Protein or peptide: Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform
    • Protein or peptide: Phosphorylase b kinase regulatory subunit beta
    • Protein or peptide: Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
    • Protein or peptide: Calmodulin-3

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Supramolecule #1: human phosphorylase kinase - inactive state

SupramoleculeName: human phosphorylase kinase - inactive state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.469422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLL HCMIRQVDKV ESFKYSQSTK DSLHAKYNTK TCATVVGDDQ WGHLQLDATS VYLLFLAQMT ASGLHIIHSL D EVNFIQNL ...String:
MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLL HCMIRQVDKV ESFKYSQSTK DSLHAKYNTK TCATVVGDDQ WGHLQLDATS VYLLFLAQMT ASGLHIIHSL D EVNFIQNL VFYIEAAYKT ADFGIWERGD KTNQGISELN ASSVGMAKAA LEALDELDLF GVKGGPQSVI HVLADEVQHC QS ILNSLLP RASTSKEVDA SLLSVVSFPA FAVEDSQLVE LTKQEIITKL QGRYGCCRFL RDGYKTPKED PNRLYYEPAE LKL FENIEC EWPLFWTYFI LDGVFSGNAE QVQEYKEALE AVLIKGKNGV PLLPELYSVP PDRVDEEYQN PHTVDRVPMG KLPH MWGQS LYILGSLMAE GFLAPGEIDP LNRRFSTVPK PDVVVQVSIL AETEEIKTIL KDKGIYVETI AEVYPIRVQP ARILS HIYS SLGCNNRMKL SGRPYRHMGV LGTSKLYDIR KTIFTFTPQF IDQQQFYLAL DNKMIVEMLR TDLSYLCSRW RMTGQP TIT FPISHSMLDE DGTSLNSSIL AALRKMQDGY FGGARVQTGK LSEFLTTSCC THLSFMDPGP EGKLYSEDYD DNYDYLE SG NWMNDYDSTS HARCGDEVAR YLDHLLAHTA PHPKLAPTSQ KGGLDRFQAA VQTTCDLMSL VTKAKELHVQ NVHMYLPT K LFQASRPSFN LLDSPHPRQE NQVPSVRVEI HLPRDQSGEV DFKALVLQLK ETSSLQEQAD ILYMLYTMKG PDWNTELYN ERSATVRELL TELYGKVGEI RHWGLIRYIS GILRKKVEAL DEACTDLLSH QKHLTVGLPP EPREKTISAP LPYEALTQLI DEASEGDMS ISILTQEIMV YLAMYMRTQP GLFAEMFRLR IGLIIQVMAT ELAHSLRCSA EEATEGLMNL SPSAMKNLLH H ILSGKEFG VERSVRPTDS NVSPAISIHE IGAVGATKTE RTGIMQLKSE IKQVEFRRLS ISAESQSPGT SMTPSSGSFP SA YDQQSSK DSRQGQWQRR RRLDGALNRV PVGFYQKVWK VLQKCHGLSV EGFVLPSSTT REMTPGEIKF SVHVESVLNR VPQ PEYRQL LVEAILVLTM LADIEIHSIG SIIAVEKIVH IANDLFLQEQ KTLGADDTML AKDPASGICT LLYDSAPSGR FGTM TYLSK AAATYVQEFL PHSICAMQ

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.032961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGAAGLTAE VSWKVLERRA RTKRSGSVYE PLKSINLPRP DNETLWDKLD HYYRIVKSTL LLYQSPTTGL FPTKTCGGDQ KAKIQDSLY CAAGAWALAL AYRRIDDDKG RTHELEHSAI KCMRGILYCY MRQADKVQQF KQDPRPTTCL HSVFNVHTGD E LLSYEEYG ...String:
MAGAAGLTAE VSWKVLERRA RTKRSGSVYE PLKSINLPRP DNETLWDKLD HYYRIVKSTL LLYQSPTTGL FPTKTCGGDQ KAKIQDSLY CAAGAWALAL AYRRIDDDKG RTHELEHSAI KCMRGILYCY MRQADKVQQF KQDPRPTTCL HSVFNVHTGD E LLSYEEYG HLQINAVSLY LLYLVEMISS GLQIIYNTDE VSFIQNLVFC VERVYRVPDF GVWERGSKYN NGSTELHSSS VG LAKAALE AINGFNLFGN QGCSWSVIFV DLDAHNRNRQ TLCSLLPRES RSHNTDAALL PCISYPAFAL DDEVLFSQTL DKV VRKLKG KYGFKRFLRD GYRTSLEDPN RCYYKPAEIK LFDGIECEFP IFFLYMMIDG VFRGNPKQVQ EYQDLLTPVL HHTT EGYPV VPKYYYVPAD FVEYEKNNPG SQKRFPSNCG RDGKLFLWGQ ALYIIAKLLA DELISPKDID PVQRYVPLKD QRNVS MRFS NQGPLENDLV VHVALIAESQ RLQVFLNTYG IQTQTPQQVE PIQIWPQQEL VKAYLQLGIN EKLGLSGRPD RPIGCL GTS KIYRILGKTV VCYPIIFDLS DFYMSQDVFL LIDDIKNALQ FIKQYWKMHG RPLFLVLIRE DNIRGSRFNP ILDMLAA LK KGIIGGVKVH VDRLQTLISG AVVEQLDFLR ISDTEELPEF KSFEELEPPK HSKVKRQSST PSAPELGQQP DVNISEWK D KPTHEILQKL NDCSCLASQA ILLGILLKRE GPNFITKEGT VSDHIERVYR RAGSQKLWLA VRYGAAFTQK FSSSIAPHI TTFLVHGKQV TLGAFGHEEE VISNPLSPRV IQNIIYYKCN THDEREAVIQ QELVIHIGWI ISNNPELFSG MLKIRIGWII HAMEYELQI RGGDKPALDL YQLSPSEVKQ LLLDILQPQQ NGRCWLNRRQ IDGSLNRTPT GFYDRVWQIL ERTPNGIIVA G KHLPQQPT LSDMTMYEMN FSLLVEDTLG NIDQPQYRQI VVELLMVVSI VLERNPELEF QDKVDLDRLV KEAFNEFQKD QS RLKEIEK QDDMTSFYNT PPLGKRGTCS YLTKAVMNLL LEGEVKPNND DPCLIS

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: 2 / 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: 2 / 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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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: FEI FALCON IV (4k 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130725
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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