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Yorodumi- EMDB-14587: Cryo-EM structure of the human GS-GN complex in the inhibited state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14587 | |||||||||
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Title | Cryo-EM structure of the human GS-GN complex in the inhibited state | |||||||||
Map data | D2 | |||||||||
Sample |
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Function / homology | Function and homology information glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding ...glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / inclusion body / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / heart development / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Marr L / Zeqiraj E | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Mechanism of glycogen synthase inactivation and interaction with glycogenin. Authors: Laura Marr / Dipsikha Biswas / Leonard A Daly / Christopher Browning / Sarah C M Vial / Daniel P Maskell / Catherine Hudson / Jay A Bertrand / John Pollard / Neil A Ranson / Heena Khatter / ...Authors: Laura Marr / Dipsikha Biswas / Leonard A Daly / Christopher Browning / Sarah C M Vial / Daniel P Maskell / Catherine Hudson / Jay A Bertrand / John Pollard / Neil A Ranson / Heena Khatter / Claire E Eyers / Kei Sakamoto / Elton Zeqiraj / Abstract: Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS) ...Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS), where GS is activated by glucose-6-phosphate (G6P) and inactivated by phosphorylation. We describe the 2.6 Å resolution cryo-EM structure of phosphorylated human GS revealing an autoinhibited GS tetramer flanked by two GN dimers. Phosphorylated N- and C-termini from two GS protomers converge near the G6P-binding pocket and buttress against GS regulatory helices. This keeps GS in an inactive conformation mediated by phospho-Ser641 interactions with a composite "arginine cradle". Structure-guided mutagenesis perturbing interactions with phosphorylated tails led to increased basal/unstimulated GS activity. We propose that multivalent phosphorylation supports GS autoinhibition through interactions from a dynamic "spike" region, allowing a tuneable rheostat for regulating GS activity. This work therefore provides insights into glycogen synthesis regulation and facilitates studies of glycogen-related diseases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14587.map.gz | 61.3 MB | EMDB map data format | |
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Header (meta data) | emd-14587-v30.xml emd-14587.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14587_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_14587.png | 97.7 KB | ||
Masks | emd_14587_msk_1.map | 91.1 MB | Mask map | |
Others | emd_14587_additional_1.map.gz emd_14587_half_map_1.map.gz emd_14587_half_map_2.map.gz | 61.1 MB 69.7 MB 69.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14587 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14587 | HTTPS FTP |
-Validation report
Summary document | emd_14587_validation.pdf.gz | 697.4 KB | Display | EMDB validaton report |
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Full document | emd_14587_full_validation.pdf.gz | 697 KB | Display | |
Data in XML | emd_14587_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | emd_14587_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14587 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14587 | HTTPS FTP |
-Related structure data
Related structure data | 7zbnMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14587.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | D2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.71 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14587_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: C1
File | emd_14587_additional_1.map | ||||||||||||
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Annotation | C1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14587_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14587_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Glycogen synthase-Glycogenin complex
Entire | Name: Glycogen synthase-Glycogenin complex |
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Components |
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-Supramolecule #1: Glycogen synthase-Glycogenin complex
Supramolecule | Name: Glycogen synthase-Glycogenin complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 485 KDa |
-Macromolecule #1: Glycogen [starch] synthase, muscle
Macromolecule | Name: Glycogen [starch] synthase, muscle / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycogen(starch) synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.88543 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MPLNRTLSMS SLPGLEDWED EFDLENAVLF EVAWEVANKV GGIYTVLQTK AKVTGDEWGD NYFLVGPYTE QGVRTQVELL EAPTPALKR TLDSMNSKGC KVYFGRWLIE GGPLVVLLDV GASAWALERW KGELWDTCNI GVPWYDREAN DAVLFGFLTT W FLGEFLAQ ...String: MPLNRTLSMS SLPGLEDWED EFDLENAVLF EVAWEVANKV GGIYTVLQTK AKVTGDEWGD NYFLVGPYTE QGVRTQVELL EAPTPALKR TLDSMNSKGC KVYFGRWLIE GGPLVVLLDV GASAWALERW KGELWDTCNI GVPWYDREAN DAVLFGFLTT W FLGEFLAQ SEEKPHVVAH FHEWLAGVGL CLCRARRLPV ATIFTTHATL LGRYLCAGAV DFYNNLENFN VDKEAGERQI YH RYCMERA AAHCAHVFTT VSQITAIEAQ HLLKRKPDIV TPNGLNVKKF SAMHEFQNLH AQSKARIQEF VRGHFYGHLD FNL DKTLYF FIAGRYEFSN KGADVFLEAL ARLNYLLRVN GSEQTVVAFF IMPARTNNFN VETLKGQAVR KQLWDTANTV KEKF GRKLY ESLLVGSLPD MNKMLDKEDF TMMKRAIFAT QRQSFPPVCT HNMLDDSSDP ILTTIRRIGL FNSSADRVKV IFHPE FLSS TSPLLPVDYE EFVRGCHLGV FPSYYEPWGY TPAECTVMGI PSISTNLSGF GCFMEEHIAD PSAYGIYILD RRFRSL DDS CSQLTSFLYS FCQQSRRQRI IQRNRTERLS DLLDWKYLGR YYMSARHMAL SKAFPEHFTY EPNEADAAQG YRYPRPA SV PPSPSLSRHS SPHQSEDEED PRNGPLEEDG ERYDEDEEAA KDRRNIRAPE WPRRASCTSS TSGSKRNSVD TATSSSLS T PSEPLSPTSS LGEERN |
-Macromolecule #2: Glycogen [starch] synthase, muscle
Macromolecule | Name: Glycogen [starch] synthase, muscle / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycogen(starch) synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.965406 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MPLNRTLSMS SLPGLEDWED EFDLENAVLF EVAWEVANKV GGIYTVLQTK AKVTGDEWGD NYFLVGPYTE QGVRTQVELL EAPTPALKR TLDSMNSKGC KVYFGRWLIE GGPLVVLLDV GASAWALERW KGELWDTCNI GVPWYDREAN DAVLFGFLTT W FLGEFLAQ ...String: MPLNRTLSMS SLPGLEDWED EFDLENAVLF EVAWEVANKV GGIYTVLQTK AKVTGDEWGD NYFLVGPYTE QGVRTQVELL EAPTPALKR TLDSMNSKGC KVYFGRWLIE GGPLVVLLDV GASAWALERW KGELWDTCNI GVPWYDREAN DAVLFGFLTT W FLGEFLAQ SEEKPHVVAH FHEWLAGVGL CLCRARRLPV ATIFTTHATL LGRYLCAGAV DFYNNLENFN VDKEAGERQI YH RYCMERA AAHCAHVFTT VSQITAIEAQ HLLKRKPDIV TPNGLNVKKF SAMHEFQNLH AQSKARIQEF VRGHFYGHLD FNL DKTLYF FIAGRYEFSN KGADVFLEAL ARLNYLLRVN GSEQTVVAFF IMPARTNNFN VETLKGQAVR KQLWDTANTV KEKF GRKLY ESLLVGSLPD MNKMLDKEDF TMMKRAIFAT QRQSFPPVCT HNMLDDSSDP ILTTIRRIGL FNSSADRVKV IFHPE FLSS TSPLLPVDYE EFVRGCHLGV FPSYYEPWGY TPAECTVMGI PSISTNLSGF GCFMEEHIAD PSAYGIYILD RRFRSL DDS CSQLTSFLYS FCQQSRRQRI IQRNRTERLS DLLDWKYLGR YYMSARHMAL SKAFPEHFTY EPNEADAAQG YRYPRPA (SEP)V PPSPSLSRHS SPHQSEDEED PRNGPLEEDG ERYDEDEEAA KDRRNIRAPE WPRRASCTSS TSGSKRNSVD TATS SSLST PSEPLSPTSS LGEERN |
-Macromolecule #3: Isoform GN-1 of Glycogenin-1
Macromolecule | Name: Isoform GN-1 of Glycogenin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: glycogenin glucosyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.469348 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MADQAFVTLT TNDAYAKGAL VLGSSLKQHR TTRRLVVLAT PQVSDSMRKV LETVFDEVIM VDVLDSGDSA HLTLMKRPEL GVTLTKLHC WSLTQYSKCV FMDADTLVLA NIDDLFDREE LSAAPDPGWP DCFNSGVFVY QPSVETYNQL LHLASEQGSF D GGDQGILN ...String: MADQAFVTLT TNDAYAKGAL VLGSSLKQHR TTRRLVVLAT PQVSDSMRKV LETVFDEVIM VDVLDSGDSA HLTLMKRPEL GVTLTKLHC WSLTQYSKCV FMDADTLVLA NIDDLFDREE LSAAPDPGWP DCFNSGVFVY QPSVETYNQL LHLASEQGSF D GGDQGILN TFFSSWATTD IRKHLPFIYN LSSISIFSYL PAFKVFGASA KVVHFLGRVK PWNYTYDPKT KSVKSEAHDP NM THPEFLI LWWNIFTTNV LPLLQQFGLV KDTCSYVNVE DVSGAISHLS LGEIPAMAQP FVSSEERKER WEQGQADYMG ADS FDNIKR KLDTYLQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 34.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |