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- EMDB-39700: Human GYS1-GYG2 complex (apo) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39700
TitleHuman GYS1-GYG2 complex (apo)
Map data
Sample
  • Complex: Human GYS1-GYG2 complex (apo)
    • Protein or peptide: Glycogen [starch] synthase, muscle
    • Protein or peptide: Glycogenin-2
KeywordsGlycogen / Glycogenin / Glycogen synthase / TRANSFERASE
Function / homology
Function and homology information


Glycogen storage disease type 0 (liver GYS2) / Glycogen storage disease type IV (GBE1) / glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding ...Glycogen storage disease type 0 (liver GYS2) / Glycogen storage disease type IV (GBE1) / glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / 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 / heart development / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase / : / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Glycogenin-2 / Glycogen [starch] synthase, muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen PP / Hsia KC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Human GYS1-GYG2 complex (apo)
Authors: Chen PP / Hsia KC
History
DepositionApr 9, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39700.png

Downloads & links

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Map

FileDownload / File: emd_39700.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-3.479568 - 4.9131556
Average (Standard dev.)-0.00065866014 (±0.08936336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39700_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39700_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 GYS1-GYG2 complex (apo)

EntireName: Human GYS1-GYG2 complex (apo)
Components
  • Complex: Human GYS1-GYG2 complex (apo)
    • Protein or peptide: Glycogen [starch] synthase, muscle
    • Protein or peptide: Glycogenin-2

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Supramolecule #1: Human GYS1-GYG2 complex (apo)

SupramoleculeName: Human GYS1-GYG2 complex (apo) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycogen [starch] synthase, muscle

MacromoleculeName: Glycogen [starch] synthase, muscle / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glycogen(starch) synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.987781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMPLNR TLSMSSLPGL EDWEDEFDLE NAVLFEVAWE VANKVGGIYT VLQTKAKVTG DEWGDNYFL VGPYTEQGVR TQVELLEAPT PALKRTLDSM NSKGCKVYFG RWLIEGGPLV VLLDVGASAW ALERWKGELW D TCNIGVPW ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMPLNR TLSMSSLPGL EDWEDEFDLE NAVLFEVAWE VANKVGGIYT VLQTKAKVTG DEWGDNYFL VGPYTEQGVR TQVELLEAPT PALKRTLDSM NSKGCKVYFG RWLIEGGPLV VLLDVGASAW ALERWKGELW D TCNIGVPW YDREANDAVL FGFLTTWFLG EFLAQSEEKP HVVAHFHEWL AGVGLCLCRA RRLPVATIFT THATLLGRYL CA GAVDFYN NLENFNVDKE AGERQIYHRY CMERAAAHCA HVFTTVSQIT AIEAQHLLKR KPDIVTPNGL NVKKFSAMHE FQN LHAQSK ARIQEFVRGH FYGHLDFNLD KTLYFFIAGR YEFSNKGADV FLEALARLNY LLRVNGSEQT VVAFFIMPAR TNNF NVETL KGQAVRKQLW DTANTVKEKF GRKLYESLLV GSLPDMNKML DKEDFTMMKR AIFATQRQSF PPVCTHNMLD DSSDP ILTT IRRIGLFNSS ADRVKVIFHP EFLSSTSPLL PVDYEEFVRG CHLGVFPSYY EPWGYTPAEC TVMGIPSIST NLSGFG CFM EEHIADPSAY GIYILDRRFR SLDDSCSQLT SFLYSFCQQS RRQRIIQRNR TERLSDLLDW KYLGRYYMSA RHMALSK AF PEHFTYEPNE ADAAQGYRYP RPASVPPSPS LSRHSSPHQS EDEEDPRNGP LEEDGERYDE DEEAAKDRRN IRAPEWPR R ASCTSSTSGS KRNSVDTATS SSLSTPSEPL SPTSSLGEER N

UniProtKB: Glycogen [starch] synthase, muscle

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Macromolecule #2: Glycogenin-2

MacromoleculeName: Glycogenin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: glycogenin glucosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.207566 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSETEFHHGA QAGLELLRSS NSPTSASQSA GMTVTDQAFV TLATNDIYCQ GALVLGQSLR RHRLTRKLVV LITPQVSSLL RVILSKVFD EVIEVNLIDS ADYIHLAFLK RPELGLTLTK LHCWTLTHYS KCVFLDADTL VLSNVDELFD RGEFSAAPDP G WPDCFNSG ...String:
MSETEFHHGA QAGLELLRSS NSPTSASQSA GMTVTDQAFV TLATNDIYCQ GALVLGQSLR RHRLTRKLVV LITPQVSSLL RVILSKVFD EVIEVNLIDS ADYIHLAFLK RPELGLTLTK LHCWTLTHYS KCVFLDADTL VLSNVDELFD RGEFSAAPDP G WPDCFNSG VFVFQPSLHT HKLLLQHAME HGSFDGADQG LLNSFFRNWS TTDIHKHLPF IYNLSSNTMY TYSPAFKQFG SS AKVVHFL GSMKPWNYKY NPQSGSVLEQ GSASSSQHQA AFLHLWWTVY QNNVLPLYKS VQAGEARASP GHTLCHSDVG GPC ADSASG VGEPCENSTP SAGVPCANSP LGSNQPAQGL PEPTQIVDET LSLPEGRRSE DMIACPETET PAVITCDPLS QPSP QPADF TETETILPAN KVESVSSEET FEPSQELPAE ALRDPSLQDA LEVVDLAVSV SQISIEEKVK ELSPEEERRK WEEGR IDYM GKDAFARIQE KLDRFLQ

UniProtKB: Glycogenin-2

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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: 7.4
Details: 50 mM K-phosphate buffer pH7.4, 150 mM NaCl, 1 mM beta-Me
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8cvz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238004
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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