[English] 日本語
Yorodumi
- EMDB-39781: human phosphorylase kinase - phosphorylation and Ca2+ bound state -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / vesicle / carbohydrate metabolic process / transmembrane transporter binding / 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: 3.74 Å
AuthorsMa R / Yan K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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

-
Structure visualization

Supplemental images

emd_39781.png

Downloads & links

-
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)

Slices (1/2)

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 °

-
Supplemental data

-
Mask #1

Fileemd_39781_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
Half map: half map

Fileemd_39781_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more