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- EMDB-28263: Cryo-EM structure of human liver glycogen phosphorylase -

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Basic information

Entry
Database: EMDB / ID: EMD-28263
TitleCryo-EM structure of human liver glycogen phosphorylase
Map data
Sample
  • Complex: Glycogen Phosphorylase
    • Protein or peptide: Glycogen phosphorylase, liver form
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
KeywordsGlycogen Phosphorylase / PLP / HYDROLASE
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / bile acid binding / glycogen catabolic process ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / bile acid binding / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site.
Similarity search - Domain/homology
Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSu C / Lyu M / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2023
Title: High-resolution structural-omics of human liver enzymes.
Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu /
Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
History
DepositionSep 28, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28263.png

Downloads & links

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Map

FileDownload / File: emd_28263.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9994271 - 2.8791687
Average (Standard dev.)-0.000022685865 (±0.054636102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28263_msk_1.map
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Half map: #2

Fileemd_28263_half_map_1.map
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Half map: #1

Fileemd_28263_half_map_2.map
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Sample components

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Entire : Glycogen Phosphorylase

EntireName: Glycogen Phosphorylase
Components
  • Complex: Glycogen Phosphorylase
    • Protein or peptide: Glycogen phosphorylase, liver form
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Glycogen Phosphorylase

SupramoleculeName: Glycogen Phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycogen phosphorylase, liver form

MacromoleculeName: Glycogen phosphorylase, liver form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycogen phosphorylase
Source (natural)Organism: Homo sapiens (human) / Organ: liver
Molecular weightTheoretical: 95.376406 KDa
SequenceString: MAKPLTDQEK RRQISIRGIV GVENVAELKK SFNRHLHFTL VKDRNVATTR DYYFALAHTV RDHLVGRWIR TQQHYYDKCP KRVYYLSLE FYMGRTLQNT MINLGLQNAC DEAIYQLGLD IEELEEIEED AGLGNGGLGR LAACFLDSMA TLGLAAYGYG I RYEYGIFN ...String:
MAKPLTDQEK RRQISIRGIV GVENVAELKK SFNRHLHFTL VKDRNVATTR DYYFALAHTV RDHLVGRWIR TQQHYYDKCP KRVYYLSLE FYMGRTLQNT MINLGLQNAC DEAIYQLGLD IEELEEIEED AGLGNGGLGR LAACFLDSMA TLGLAAYGYG I RYEYGIFN QKIRDGWQVE EADDWLRYGN PWEKSRPEFM LPVHFYGKVE HTNTGTKWID TQVVLALPYD TPVPGYMNNT VN TMRLWSA RAPNDFNLRD FNVGDYIQAV LDRNLAENIS RVLYPNDNFF EGKELRLKQE YFVVAATLQD IIRRFKASKF GST RGAGTV FDAFPDQVAI QLNDTHPALA IPELMRIFVD IEKLPWSKAW ELTQKTFAYT NHTVLPEALE RWPVDLVEKL LPRH LEIIY EINQKHLDRI VALFPKDVDR LRRMSLIEEE GSKRINMAHL CIVGSHAVNG VAKIHSDIVK TKVFKDFSEL EPDKF QNKT NGITPRRWLL LCNPGLAELI AEKIGEDYVK DLSQLTKLHS FLGDDVFLRE LAKVKQENKL KFSQFLETEY KVKINP SSM FDVQVKRIHE YKRQLLNCLH VITMYNRIKK DPKKLFVPRT VIIGGKAAPG YHMAKMIIKL ITSVADVVNN DPMVGSK LK VIFLENYRVS LAEKVIPATD LSEQISTAGT EASGTGNMKF MLNGALTIGT MDGANVEMAE EAGEENLFIF GMRIDDVA A LDKKGYEAKE YYEALPELKL VIDQIDNGFF SPKQPDLFKD IINMLFYHDR FKVFADYEAY VKCQDKVSQL YMNPKAWNT MVLKNIAASG KFSSDRTIKE YAQNIWNVE

UniProtKB: Glycogen phosphorylase, liver form

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 764806
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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