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Open data
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Basic information
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Title | Cryo-EM structure of human liver glucosidase II | |||||||||
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![]() | glucosidase II / GANAB / glycosyl hydrolase 31 family / HYDROLASE | |||||||||
Function / homology | ![]() 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 / phosphoprotein binding / protein kinase C 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
![]() | Su C / Lyu M / Zhang Z / Yu EW | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.7 KB | Display | ![]() |
Images | ![]() | 144.5 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 3 MB 95.7 MB 95.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8emrMC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8em2C ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eojC ![]() 8eorC ![]() 23434 M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: density modification map
File | emd_28262_additional_1.map | ||||||||||||
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Annotation | density modification map | ||||||||||||
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-Half map: #2
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-Half map: #1
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Density Histograms |
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Sample components
-Entire : glucosidase II
Entire | Name: glucosidase II |
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Components |
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-Supramolecule #1: glucosidase II
Supramolecule | Name: glucosidase II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Neutral alpha-glucosidase AB
Macromolecule | Name: Neutral alpha-glucosidase AB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mannosyl-oligosaccharide alpha-1,3-glucosidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 106.997828 KDa |
Sequence | String: 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 |
-Macromolecule #2: Glucosidase 2 subunit beta
Macromolecule | Name: Glucosidase 2 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 59.485223 KDa |
Sequence | String: 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 |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |