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Open data
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Basic information
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Title | Cryo-EM structure of human PRDX4 | |||||||||
![]() | Cryo-EM structure of human PRDX4 | |||||||||
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![]() | OXIDOREDUCTASE | |||||||||
Function / homology | ![]() cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process ...cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / spermatogenesis / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / molecular adaptor activity / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
![]() | Su CC / Lyu M | |||||||||
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 | ![]() | 97.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 9.8 KB 13 KB | Display Display | ![]() |
Images | ![]() | 152.3 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() ![]() | 51.8 MB 95.7 MB 95.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 955.1 KB | Display | ![]() |
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Full document | ![]() | 954.6 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ekwMC ![]() 7uzmC ![]() 8ekyC ![]() 8em2C ![]() 8emrC ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eojC ![]() 8eorC ![]() 23432 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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Map
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Annotation | Cryo-EM structure of human PRDX4 | ||||||||||||||||||||
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: unsharpened map
File | emd_28214_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Cryo-EM structure of human PRDX4
File | emd_28214_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of human PRDX4 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of human PRDX4
File | emd_28214_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of human PRDX4 | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Peroxiredoxin-4
Macromolecule | Name: Peroxiredoxin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
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: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 402 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: 29.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / 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
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8ekw: |