+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28217 | |||||||||
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Title | Cryo-EM structure of the human PRDX4-ErP46 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Peroxiredoxin-4 / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / cellular response to stress / protein disulfide-isomerase / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / protein maturation by protein folding / Lysosome Vesicle Biogenesis ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / cellular response to stress / protein disulfide-isomerase / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / protein maturation by protein folding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / extracellular matrix organization / lysosomal lumen / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / azurophil granule lumen / protein folding / spermatogenesis / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / molecular adaptor activity / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Su CC / Lyu M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28217.map.gz | 97.4 MB | EMDB map data format | |
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Header (meta data) | emd-28217-v30.xml emd-28217.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28217_fsc.xml emd_28217_fsc_2.xml | 9.9 KB 13.8 KB | Display Display | FSC data file |
Images | emd_28217.png | 103.2 KB | ||
Masks | emd_28217_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-28217.cif.gz | 5.5 KB | ||
Others | emd_28217_additional_1.map.gz emd_28217_half_map_1.map.gz emd_28217_half_map_2.map.gz | 51.8 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28217 | HTTPS FTP |
-Related structure data
Related structure data | 8ekyMC 7uzmC 8ekwC 8em2C 8emrC 8emsC 8emtC 8eneC 8eojC 8eorC 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_28217.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_28217_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Unsharpened map
File | emd_28217_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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-Half map: #2
File | emd_28217_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_28217_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : H6PD
Entire | Name: H6PD |
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Components |
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-Supramolecule #1: H6PD
Supramolecule | Name: H6PD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Peroxiredoxin-4
Macromolecule | Name: Peroxiredoxin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: thioredoxin-dependent peroxiredoxin |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 30.578873 KDa |
Sequence | String: MEALPLLAAT TPDHGRHRRL LLLPLLLFLL PAGAVQGWET EERPRTREEE CHFYAGGQVY PGEASRVSVA DHSLHLSKAK ISKPAPYWE GTAVIDGEFK ELKLTDYRGK YLVFFFYPLD FTFVCPTEII AFGDRLEEFR SINTEVVACS VDSQFTHLAW I NTPRRQGG ...String: MEALPLLAAT TPDHGRHRRL LLLPLLLFLL PAGAVQGWET EERPRTREEE CHFYAGGQVY PGEASRVSVA DHSLHLSKAK ISKPAPYWE GTAVIDGEFK ELKLTDYRGK YLVFFFYPLD FTFVCPTEII AFGDRLEEFR SINTEVVACS VDSQFTHLAW I NTPRRQGG LGPIRIPLLS DLTHQISKDY GVYLEDSGHT LRGLFIIDDK GILRQITLND LPVGRSVDET LRLVQAFQYT DK HGEVCPA GWKPGSETII PDPAGKLKYF DKLN UniProtKB: Peroxiredoxin-4 |
-Macromolecule #2: Thioredoxin domain-containing protein 5
Macromolecule | Name: Thioredoxin domain-containing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.687727 KDa |
Sequence | String: MPARPGRLLP LLARPAALTA LLLLLLGHGG GGRWGARAQE AAAAAADGPP AADGEDGQDP HSKHLYTADM FTHGIQSAAH FVMFFAPWC GHCQRLQPTW NDLGDKYNSM EDAKVYVAKV DCTAHSDVCS AQGVRGYPTL KLFKPGQEAV KYQGPRDFQT L ENWMLQTL ...String: MPARPGRLLP LLARPAALTA LLLLLLGHGG GGRWGARAQE AAAAAADGPP AADGEDGQDP HSKHLYTADM FTHGIQSAAH FVMFFAPWC GHCQRLQPTW NDLGDKYNSM EDAKVYVAKV DCTAHSDVCS AQGVRGYPTL KLFKPGQEAV KYQGPRDFQT L ENWMLQTL NEEPVTPEPE VEPPSAPELK QGLYELSASN FELHVAQGDH FIKFFAPWCG HCKALAPTWE QLALGLEHSE TV KIGKVDC TQHYELCSGN QVRGYPTLLW FRDGKKVDQY KGKRDLESLR EYVESQLQRT ETGATETVTP SEAPVLAAEP EAD KGTVLA LTENNFDDTI AEGITFIKFY APWCGHCKTL APTWEELSKK EFPGLAGVKI AEVDCTAERN ICSKYSVRGY PTLL LFRGG KKVSEHSGGR DLDSLHRFVL SQAKDEL UniProtKB: Thioredoxin domain-containing protein 5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | This is from a heterogeneous and impure protein sample. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 29.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8eky: |