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Open data
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Basic information
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Title | Cryo-EM structure of the human PRDX4-ErP46 complex | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 97.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 9.9 KB 13.8 KB | Display Display | ![]() |
Images | ![]() | 103.2 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() ![]() | 51.8 MB 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | 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 ( |
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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: Unsharpened map
File | emd_28217_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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-Half map: #2
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-Half map: #1
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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: all |
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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 / EC number: thioredoxin-dependent peroxiredoxin |
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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: ![]() |
-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: ![]() |
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Source (natural) | Organism: ![]() ![]() |
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 | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8eky: |