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- EMDB-39785: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - ph... -

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Basic information

Entry
Database: EMDB / ID: EMD-39785
Titlehuman phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
Map data
Sample
  • Complex: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
    • Other: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
KeywordsKinase / glycogenolysis / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 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_39785.png

Downloads & links

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Map

FileDownload / File: emd_39785.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.14
Minimum - Maximum-2.0224187 - 3.6173754
Average (Standard dev.)-0.00004362542 (±0.0796912)
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_39785_msk_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_39785_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39785_half_map_2.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 alpha/beta/gamma/delta subcomplex - ph...

EntireName: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
Components
  • Complex: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
    • Other: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state

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Supramolecule #1: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - ph...

SupramoleculeName: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - ph...

MacromoleculeName: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLLH CMIRQVDKVE (SEP)FKY(SEP)Q(SEP)TKD (SEP)LHAKYNTKT CATVVGDDQW GHLQLDATSV YLLFLAQMTA SGLHIIHSLD ...String:
MRSRSNSGVR LDGYARLVQQ TILCHQNPVT GLLPASYDQK DAWVRDNVYS ILAVWGLGLA YRKNADRDED KAKAYELEQS VVKLMRGLLH CMIRQVDKVE (SEP)FKY(SEP)Q(SEP)TKD (SEP)LHAKYNTKT CATVVGDDQW GHLQLDATSV YLLFLAQMTA SGLHIIHSLD EVNFIQNLVF YIEAAYKTAD FGIWERGDKT NQGISELNAS (SEP)VGMAKAALE ALDELDLFGV KGGPQSVIHV LADEVQHCQ(SEP) ILNSLLPRAS TSKEVDASLL SVVSFPAFAV EDSQLVELTK QEIITKLQGR YGCCRFLRDG YKTPKEDPNR LYYEPAELKL FENIECEWPL FWTYFILDGV FSGNAEQVQE YKEALEAVLI KGKNGVPLLP ELY(SEP)VPPDRV DEEYQNPHTV DRVPMGKLPH MWGQSLYILG SLMAEGFLAP GEIDPLNRRF STVPKPDVVV QVSILAETEE IKTILKDKGI YVETIAEVYP IRVQPARIL(SEP) HIYSSLGCNN RMKLSGRPYR HMGVLGTSKL YDIRKTIFTF TPQFIDQQQF YLALDNKMIV EMLRTDL(SEP)YL CSRWRMTGQP TITFPISHSM LDEDGTSLNS SILAALRKMQ DGYFGGARVQ TGKLSEFLTT SCCTHLSFMD PGPEGKLY(SEP)E DYDDNYDYLE SGNWMNDYDS TSHARCGDEV ARYLDHLLAH (TPO)APHPKLAPT SQKGGLDRFQ AAVQTTCDLM (SEP)LVTKAKELH VQNVHMYLPT KLFQA(SEP)RP(SEP)F NLLD(SEP)PHPRQ ENQVP(SEP)VRVE IHLPRDQ(SEP)GE VDFKALVLQL KETSSLQEQA DILYMLYTMK GPDWNTELYN ERSATVRELL TELYGKVGEI RHWGLIRYIS GILRKKVEAL DEACTDLLSH QKHL(TPO)VGLPP EPREKTISAP LPYEALTQLI DEASEGDMSI SILTQEIMVY LAMYMRTQPG LFAEMFRLRI GLIIQVMATE LAHSLRCSAE EATEGLMNLS PSAMKNLLHH IL(SEP)GKEFGVE R(SEP)VRPTDSNV (SEP)PAI(SEP)IHEIG AVGA(TPO)KTER(TPO) GIMQLK(SEP)EIK QVEFRRL(SEP)I(SEP) AE(SEP)Q(SEP)PGTSM (TPO)PSSGSFPSA YDQQSSKDSR QGQWQRRRRL DGALNRVPVG FYQKVWKVLQ KCHGLSVEGF VLPSSTTREM TPGEIKFSVH VESVLNRVPQ PEYRQLLVEA ILVLTMLADI EIHSIGSIIA VEKIVHIAND LFLQEQKTLG ADD(TPO)MLAKDP ASGICTLLYD SAP(SEP)GRFGTM TYLSKAAATY VQEFLPH(SEP)IC AMQMAGAAGL TAEV(SEP)WKVLE RRARTKR(SEP)G(SEP) VYEPLK(SEP)INL PRPDNETLWD KLDHYYRIVK STLLLYQSPT TGLFPTKTCG GDQKAKIQDS LYCAAGAWAL ALAYRRIDDD KGRTHELEHS AIKCMRGILY CYMRQADKVQ QFKQDPRPTT CLHSVFNVHT GDELLSYEEY GHLQINAVSL YLLYLVEMIS SGLQIIYNTD EVSFIQNLVF CVERVYRVPD FGVWERGSKY NNGSTELHSS (SEP)VGLAKAALE AINGFNLFGN QGCSWSVIFV DLDAHNRNRQ (TPO)LC(SEP)LLPRES RSHNTDAALL PCI(SEP)YPAFAL DDEVLFSQTL DKVVRKLKGK YGFKRFLRDG YRTSLEDPNR CYYKPAEIKL FDGIECEFPI FFLYMMIDGV FRGNPKQVQE YQDLLTPVLH HTTEGYPVVP KYYYVPADFV EYEKNNPGSQ KRFPSNCGRD GKLFLWGQAL YIIAKLLADE LISPKDIDPV QRYVPLKDQR NVSMRFSNQG PLENDLVVHV ALIAESQRLQ VFLNTYGIQT QTPQQVEPIQ IWPQQELVKA YLQLGINEKL GLSGRPDRPI GCLGTSKIYR ILGKTVVCYP IIFDLSDFYM SQDVFLLIDD IKNALQFIKQ YWKMHGRPLF LVLIREDNIR GSRFNPILDM LAALKKGIIG GVKVHVDRLQ TLISGAVVEQ LDFLRISDTE ELPEFK(SEP)FEE LEPPKHSKVK RQ(SEP)(SEP)TPSAPE LGQQPDVNIS EWKDKPTHEI LQKLNDCSCL ASQAILLGIL LKREGPNFIT KEGTV(SEP)DHIE RVYRRAGSQK LWLAVRYGAA FTQKFSSSIA PHITTFLVHG KQVTLGAFGH EEEVISNPLS PRVIQNIIYY KCNTHDEREA VIQQELVIHI GWIISNNPEL FSGMLKIRIG WIIHAMEYEL QIRGGDKPAL DLYQLSPSEV KQLLLDILQP QQNGRCWLNR RQIDGSLNRT PTGFYDRVWQ ILERTPNGII VAGKHLPQQP TLSDMTMYEM NFSLLVEDTL GNIDQPQYRQ IVVELLMVVS IVLERNPELE FQDKVDLDRL VKEAFNEFQK DQSRLKEIEK QDDMT(SEP)FYNT PPLGKRG(TPO)CS YLTKAVMNLL LEGEVKPNND DPCLISMTRD EALPDSHSAQ DFYENYEPKE ILGRGVSSVV RRCIHKPTSQ EYAVKVIDVT GGGSFSPEEV RELREATLKE VDILRKVSGH PNIIQLKDTY ETNTFFFLVF DLMKRGELFD YLTEKVTLSE KETRKIMRAL LEVICTLHKL NIVHRDLKPE NILLDDNMNI KLTDFGFSCQ LEPGERLREV CGTPSYLAPE IIECSMNEDH PGYGKEVDMW STGVIMYTLL AGSPPFWHRK QMLMLRMIMS GNYQFGSPEW DDYSDTVKDL VSRFLVVQPQ NRYTAEEALA HPFFQQYLVE EVRHFSPRGK FKVIALTVLA SVRIYYQYRR VKPVTREIVI RDPYALRPLR RLIDAYAFRI YGHWVKKGQQ QNRAALFENT PKAVLLSLAE EDYYKDDDDK SGPDEVDASG RMADQLTEEQ IAEFKEAFSL FDKDGDGTIT TKELGTVMRS LGQNPTEAEL QDMINEVDAD GNGTIDFPEF LTMMARKMKD TDSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK
Recombinant expressionOrganism: Homo sapiens (human)

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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: 3.23 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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