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- EMDB-28262: Cryo-EM structure of human liver glucosidase II -

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Basic information

Entry
Database: EMDB / ID: EMD-28262
TitleCryo-EM structure of human liver glucosidase II
Map data
Sample
  • Complex: glucosidase II
    • Protein or peptide: Neutral alpha-glucosidase AB
    • Protein or peptide: Glucosidase 2 subunit beta
  • Ligand: CALCIUM ION
Keywordsglucosidase II / GANAB / glycosyl hydrolase 31 family / HYDROLASE
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / Calnexin/calreticulin cycle / glucosidase II complex / alpha-glucosidase activity / Maturation of spike protein / N-glycan processing / Advanced glycosylation endproduct receptor signaling / liver development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / Calnexin/calreticulin cycle / glucosidase II complex / alpha-glucosidase activity / Maturation of spike protein / N-glycan processing / Advanced glycosylation endproduct receptor signaling / liver development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / protein kinase C binding / phosphoprotein binding / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / carbohydrate binding / Maturation of spike protein / transmembrane transporter binding / carbohydrate metabolic process / intracellular signal transduction / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / calcium ion binding / Golgi apparatus / endoplasmic reticulum / RNA binding / extracellular exosome / membrane
Similarity search - Function
Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain ...Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / EF hand / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Endoplasmic reticulum targeting sequence. / LDL receptor-like superfamily / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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_28262.png

Downloads & links

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Map

FileDownload / File: emd_28262.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.5757246 - 1.7632291
Average (Standard dev.)-0.0006098593 (±0.029527837)
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_28262_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: density modification map

Fileemd_28262_additional_1.map
Annotationdensity modification map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28262_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28262_half_map_2.map
Projections & Slices
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Sample components

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Entire : glucosidase II

EntireName: glucosidase II
Components
  • Complex: glucosidase II
    • Protein or peptide: Neutral alpha-glucosidase AB
    • Protein or peptide: Glucosidase 2 subunit beta
  • Ligand: CALCIUM ION

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Supramolecule #1: glucosidase II

SupramoleculeName: glucosidase II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neutral alpha-glucosidase AB

MacromoleculeName: Neutral alpha-glucosidase AB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mannosyl-oligosaccharide alpha-1,3-glucosidase
Source (natural)Organism: Homo sapiens (human) / Organ: liver
Molecular weightTheoretical: 106.997828 KDa
SequenceString: MAAVAAVAAR RRRSWASLVL AFLGVCLGIT LAVDRSNFKT CEESSFCKRQ RSIRPGLSPY RALLDSLQLG PDSLTVHLIH EVTKVLLVL ELQGLQKNMT RFRIDELEPR RPRYRVPDVL VADPPIARLS VSGRDENSVE LTMAEGPYKI ILTARPFRLD L LEDRSLLL ...String:
MAAVAAVAAR RRRSWASLVL AFLGVCLGIT LAVDRSNFKT CEESSFCKRQ RSIRPGLSPY RALLDSLQLG PDSLTVHLIH EVTKVLLVL ELQGLQKNMT RFRIDELEPR RPRYRVPDVL VADPPIARLS VSGRDENSVE LTMAEGPYKI ILTARPFRLD L LEDRSLLL SVNARGLLEF EHQRAPRVSQ GSKDPAEGDG AQPEETPRDG DKPEETQGKA EKDEPGAWEE TFKTHSDSKP YG PMSVGLD FSLPGMEHVY GIPEHADNLR LKVTEGGEPY RLYNLDVFQY ELYNPMALYG SVPVLLAHNP HRDLGIFWLN AAE TWVDIS SNTAGKTLFG KMMDYLQGSG ETPQTDVRWM SETGIIDVFL LLGPSISDVF RQYASLTGTQ ALPPLFSLGY HQSR WNYRD EADVLEVDQG FDDHNLPCDV IWLDIEHADG KRYFTWDPSR FPQPRTMLER LASKRRKLVA IVDPHIKVDS GYRVH EELR NLGLYVKTRD GSDYEGWCWP GSAGYPDFTN PTMRAWWANM FSYDNYEGSA PNLFVWNDMN EPSVFNGPEV TMLKDA QHY GGWEHRDVHN IYGLYVHMAT ADGLRQRSGG MERPFVLARA FFAGSQRFGA VWTGDNTAEW DHLKISIPMC LSLGLVG LS FCGADVGGFF KNPEPELLVR WYQMGAYQPF FRAHAHLDTG RREPWLLPSQ HNDIIRDALG QRYSLLPFWY TLLYQAHR E GIPVMRPLWV QYPQDVTTFN IDDQYLLGDA LLVHPVSDSG AHGVQVYLPG QGEVWYDIQS YQKHHGPQTL YLPVTLSSI PVFQRGGTIV PRWMRVRRSS ECMKDDPITL FVALSPQGTA QGELFLDDGH TFNYQTRQEF LLRRFSFSGN TLVSSSADPE GHFETPIWI ERVVIIGAGK PAAVVLQTKG SPESRLSFQH DPETSVLVLR KPGINVASDW SIHLR

UniProtKB: Neutral alpha-glucosidase AB

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Macromolecule #2: Glucosidase 2 subunit beta

MacromoleculeName: Glucosidase 2 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: liver
Molecular weightTheoretical: 59.485223 KDa
SequenceString: MLLPLLLLLP MCWAVEVKRP RGVSLTNHHF YDESKPFTCL DGSATIPFDQ VNDDYCDCKD GSDEPGTAAC PNGSFHCTNT GYKPLYIPS NRVNDGVCDC CDGTDEYNSG VICENTCKEK GRKERESLQQ MAEVTREGFR LKKILIEDWK KAREEKQKKL I ELQAGKKS ...String:
MLLPLLLLLP MCWAVEVKRP RGVSLTNHHF YDESKPFTCL DGSATIPFDQ VNDDYCDCKD GSDEPGTAAC PNGSFHCTNT GYKPLYIPS NRVNDGVCDC CDGTDEYNSG VICENTCKEK GRKERESLQQ MAEVTREGFR LKKILIEDWK KAREEKQKKL I ELQAGKKS LEDQVEMLRT VKEEAEKPER EAKEQHQKLW EEQLAAAKAQ QEQELAADAF KELDDDMDGT VSVTELQTHP EL DTDGDGA LSEAEAQALL SGDTQTDATS FYDRVWAAIR DKYRSEALPT DLPAPSAPDL TEPKEEQPPV PSSPTEEEEE EEE EEEEEA EEEEEEEDSE EAPPPLSPPQ PASPAEEDKM PPYDEQTQAF IDAAQEARNK FEEAERSLKD MEESIRNLEQ EISF DFGPN GEFAYLYSQC YELTTNEYVY RLCPFKLVSQ KPKLGGSPTS LGTWGSWIGP DHDKFSAMKY EQGTGCWQGP NRSTT VRLL CGKETMVTST TEPSRCEYLM ELMTPAACPE PPPEAPTEDD HDEL

UniProtKB: Glucosidase 2 subunit beta

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129601
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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