[English] 日本語
Yorodumi- EMDB-6309: Cryo-EM structure of human peroxiredoxin-3 filament reveals the a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6309 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone | |||||||||
Map data | Cryo-EM structure of human peroxiredoxin-3 filament | |||||||||
Sample |
| |||||||||
Keywords | Peroxiredoxin / 2-Cys Prx high-molecular-weight form / cryo-electron microscopy / image processing / molecular chaperone | |||||||||
Function / homology | Function and homology information peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / myeloid cell differentiation / thioredoxin peroxidase activity / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis ...peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / myeloid cell differentiation / thioredoxin peroxidase activity / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis / regulation of mitochondrial membrane potential / mitochondrion organization / hydrogen peroxide catabolic process / cellular response to reactive oxygen species / response to hydrogen peroxide / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Radjainia M / Venugopal HP / Desfosses A / Phillips AJ / Yewdall NA / Hampton MB / Gerrard JA / Mitra AK | |||||||||
Citation | Journal: Structure / Year: 2015 Title: Cryo-electron microscopy structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone. Authors: Mazdak Radjainia / Hariprasad Venugopal / Ambroise Desfosses / Amy J Phillips / N Amy Yewdall / Mark B Hampton / Juliet A Gerrard / Alok K Mitra / Abstract: Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2- ...Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2-Cys Prxs are homodimers, which can self-associate to form complex assemblies that are hypothesized to have signaling and chaperone activity. Mitochondrial Prx3 forms dodecameric toroids, which can further stack to form filaments, the so-called high-molecular-weight (HMW) form that has putative holdase activity. We used single-particle analysis and helical processing of electron cryomicroscopy images of human Prx3 filaments induced by low pH to generate a ∼7-Å resolution 3D structure of the HMW form, the first such structure for a 2-Cys Prx. The pseudo-atomic model reveals interactions that promote the stacking of the toroids and shows that unlike previously reported data, the structure can accommodate a partially folded C terminus. The HMW filament lumen displays hydrophobic patches, which we hypothesize bestow holdase activity. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6309.map.gz | 18.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6309-v30.xml emd-6309.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | 400_6309.gif 80_6309.gif | 83.8 KB 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6309 | HTTPS FTP |
-Validation report
Summary document | emd_6309_validation.pdf.gz | 79.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6309_full_validation.pdf.gz | 78.5 KB | Display | |
Data in XML | emd_6309_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6309 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6309.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM structure of human peroxiredoxin-3 filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human peroxiredoxin-3 filament
Entire | Name: Human peroxiredoxin-3 filament |
---|---|
Components |
|
-Supramolecule #1000: Human peroxiredoxin-3 filament
Supramolecule | Name: Human peroxiredoxin-3 filament / type: sample / ID: 1000 / Number unique components: 1 |
---|
-Macromolecule #1: Peroxiredoxin 3
Macromolecule | Name: Peroxiredoxin 3 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: human / Organelle: mitochondria |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Rosetta (DE3) / Recombinant plasmid: pET151 |
Sequence | UniProtKB: Thioredoxin-dependent peroxide reductase, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 4 / Details: 20 mM HEPES, 75 mM NaCl |
Grid | Details: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 3 seconds blotting time |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Date | Oct 1, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 45 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTFTILT |
---|---|
Final reconstruction | Applied symmetry - Helical parameters - Δz: 42.82 Å Applied symmetry - Helical parameters - Δ&Phi: 8.06 ° Applied symmetry - Helical parameters - Axial symmetry: D6 (2x6 fold dihedral) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: OTHER / Software - Name: BSOFT, EMAN2, SPRING / Number images used: 466320 |