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Yorodumi- EMDB-26421: Meprin alpha helix (activated) - full C1 consensus reconstruction -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26421 | |||||||||
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Title | Meprin alpha helix (activated) - full C1 consensus reconstruction | |||||||||
Map data | Unsharpened final map. Low pass filtered to the global FSC. | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Bayly-Jones C / Lupton CJ / Fritz C / Schlenzig D / Whisstock JC | |||||||||
Funding support | Germany, Australia, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Helical ultrastructure of the metalloprotease meprin α in complex with a small molecule inhibitor. Authors: Charles Bayly-Jones / Christopher J Lupton / Claudia Fritz / Hariprasad Venugopal / Daniel Ramsbeck / Michael Wermann / Christian Jäger / Alex de Marco / Stephan Schilling / Dagmar ...Authors: Charles Bayly-Jones / Christopher J Lupton / Claudia Fritz / Hariprasad Venugopal / Daniel Ramsbeck / Michael Wermann / Christian Jäger / Alex de Marco / Stephan Schilling / Dagmar Schlenzig / James C Whisstock / Abstract: The zinc-dependent metalloprotease meprin α is predominantly expressed in the brush border membrane of proximal tubules in the kidney and enterocytes in the small intestine and colon. In normal ...The zinc-dependent metalloprotease meprin α is predominantly expressed in the brush border membrane of proximal tubules in the kidney and enterocytes in the small intestine and colon. In normal tissue homeostasis meprin α performs key roles in inflammation, immunity, and extracellular matrix remodelling. Dysregulated meprin α is associated with acute kidney injury, sepsis, urinary tract infection, metastatic colorectal carcinoma, and inflammatory bowel disease. Accordingly, meprin α is the target of drug discovery programs. In contrast to meprin β, meprin α is secreted into the extracellular space, whereupon it oligomerises to form giant assemblies and is the largest extracellular protease identified to date (~6 MDa). Here, using cryo-electron microscopy, we determine the high-resolution structure of the zymogen and mature form of meprin α, as well as the structure of the active form in complex with a prototype small molecule inhibitor and human fetuin-B. Our data reveal that meprin α forms a giant, flexible, left-handed helical assembly of roughly 22 nm in diameter. We find that oligomerisation improves proteolytic and thermal stability but does not impact substrate specificity or enzymatic activity. Furthermore, structural comparison with meprin β reveal unique features of the active site of meprin α, and helical assembly more broadly. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26421.map.gz | 122 MB | EMDB map data format | |
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Header (meta data) | emd-26421-v30.xml emd-26421.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26421_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_26421.png | 70.8 KB | ||
Masks | emd_26421_msk_1.map | 244.1 MB | Mask map | |
Others | emd_26421_half_map_1.map.gz emd_26421_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26421 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26421 | HTTPS FTP |
-Validation report
Summary document | emd_26421_validation.pdf.gz | 921.1 KB | Display | EMDB validaton report |
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Full document | emd_26421_full_validation.pdf.gz | 920.6 KB | Display | |
Data in XML | emd_26421_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_26421_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26421 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26421 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26421.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Unsharpened final map. Low pass filtered to the global FSC. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26421_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map (1 of 2).
File | emd_26421_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map (1 of 2). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map (2 of 2).
File | emd_26421_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map (2 of 2). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full helical meprin alpha in the activated state
Entire | Name: Full helical meprin alpha in the activated state |
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Components |
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-Supramolecule #1: Full helical meprin alpha in the activated state
Supramolecule | Name: Full helical meprin alpha in the activated state / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all Details: Full C1 reconstruction of the filamentous helix of recombinant, secreted helical meprin alpha in the activated state |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) / Recombinant cell: Schneider-2 / Recombinant plasmid: pMT/BiP/V5 |
Molecular weight | Theoretical: 85 kDa/nm |
-Macromolecule #1: Human meprin alpha
Macromolecule | Name: Human meprin alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: meprin A |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDILLQK SR NGLRDPN TRWTFPIPYI LADNLGLNAK GAILYAFEMF RLKSCVDFKP YEGESSYIIF QQF DGCWSE VGDQHVGQNI SIGQGCAYKA IIEHEILHAL GFYHEQSRTD RDDYVNIWWD QILS ...String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDILLQK SR NGLRDPN TRWTFPIPYI LADNLGLNAK GAILYAFEMF RLKSCVDFKP YEGESSYIIF QQF DGCWSE VGDQHVGQNI SIGQGCAYKA IIEHEILHAL GFYHEQSRTD RDDYVNIWWD QILS GYQHN FDTYDDSLIT DLNTPYDYES LMHYQPFSFN KNASVPTITA KIPEFNSIIG QRLDF SAID LERLNRMYNC TTTHTLLDHC TFEKANICGM IQGTRDDTDW AHQDSAQAGE VDHTLL GQC TGAGYFMQFS TSSGSAEEAA LLESRILYPK RKQQCLQFFY KMTGSPSDRL VVWVRRD DS TGNVRKLVKV QTFQGDDDHN WKIAHVVLKE EQKFRYLFQG TKGDPQNSTG GIYLDDIT L TETPCPTGVW TVRNFSQVLE NTSKGDKLQS PRFYNSEGYG FGVTLYPNSR ESSGYLRLA FHVCSGENDA ILEWPVENRQ VIITILDQEP DVRNRMSSSM VFTTSKSHTS PAINDTVIWD RPSRVGTYH TDCNCFRSID LGWSGFISHQ MLKRRSFLKN DDLIIFVDFE DITHLS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 s blot, -3 force. | |||||||||
Details | Polydisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2648 / Average electron dose: 44.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Rigid body fit only |
Refinement | Space: REAL / Protocol: OTHER |