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- EMDB-26423: Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3... -
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Open data
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Basic information
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Title | Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide) | |||||||||
![]() | DeepEMhancer (highres) sharpened final map. Low pass filtered to global FSC. | |||||||||
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Function / homology | ![]() meprin A / meprin A complex / epidermal growth factor receptor ligand maturation / metallodipeptidase activity / signaling receptor ligand precursor processing / metalloendopeptidase activity / metallopeptidase activity / extracellular space / zinc ion binding / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
![]() | Bayly-Jones C / Lupton CJ / Fritz C / Schlenzig D / Whisstock JC | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 | ![]() | 2.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.5 KB 27.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.3 KB | Display | ![]() |
Images | ![]() | 113.6 KB | ||
Masks | ![]() | 42.9 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 38.2 MB 21.5 MB 39.8 MB 39.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 746.8 KB | Display | ![]() |
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Full document | ![]() | 746.4 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uafMC ![]() 7uabC ![]() 7uacC ![]() 7uaeC ![]() 7uaiC C: citing same article ( M: atomic model generated by this map |
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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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Annotation | DeepEMhancer (highres) sharpened final map. Low pass filtered to 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
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Density Histograms |
-Additional map: DeepEMhancer (mask) sharpened final map. Low pass filtered...
File | emd_26423_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer (mask) sharpened final map. Low pass filtered to global FSC. | ||||||||||||
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Density Histograms |
-Additional map: Unsharpened final map. Low pass filtered to the global FSC.
File | emd_26423_additional_2.map | ||||||||||||
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Annotation | Unsharpened final map. Low pass filtered to the global FSC. | ||||||||||||
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Density Histograms |
-Half map: Unfiltered half-map (1 of 2).
File | emd_26423_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map (1 of 2). | ||||||||||||
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Density Histograms |
-Half map: Unfiltered half-map (2 of 2).
File | emd_26423_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map (2 of 2). | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Tetrameric portion of helical meprin alpha in complex with a smal...
Entire | Name: Tetrameric portion of helical meprin alpha in complex with a small molecule inhibitor |
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Components |
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-Supramolecule #1: Tetrameric portion of helical meprin alpha in complex with a smal...
Supramolecule | Name: Tetrameric portion of helical meprin alpha in complex with a small molecule inhibitor type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Localised reconstruction of tetrameric region of recombinant, secreted helical meprin alpha in complex with a small molecule inhibitor |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 85 kDa/nm |
-Macromolecule #1: Meprin A subunit alpha
Macromolecule | Name: Meprin A subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: meprin A |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 67.28582 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDILLQK SRNGLRDPNT RWTFPIPYIL ADNLGLNAKG AILYAFEMF RLKSCVDFKP YEGESSYIIF QQFDGCWSEV GDQHVGQNIS IGQGCAYKAI IEHEILHALG FYHEQSRTDR D DYVNIWWD ...String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDILLQK SRNGLRDPNT RWTFPIPYIL ADNLGLNAKG AILYAFEMF RLKSCVDFKP YEGESSYIIF QQFDGCWSEV GDQHVGQNIS IGQGCAYKAI IEHEILHALG FYHEQSRTDR D DYVNIWWD QILSGYQHNF DTYDDSLITD LNTPYDYESL MHYQPFSFNK NASVPTITAK IPEFNSIIGQ RLDFSAIDLE RL NRMYNCT TTHTLLDHCT FEKANICGMI QGTRDDTDWA HQDSAQAGEV DHTLLGQCTG AGYFMQFSTS SGSAEEAALL ESR ILYPKR KQQCLQFFYK MTGSPSDRLV VWVRRDDSTG NVRKLVKVQT FQGDDDHNWK IAHVVLKEEQ KFRYLFQGTK GDPQ NSTGG IYLDDITLTE TPCPTGVWTV RNFSQVLENT SKGDKLQSPR FYNSEGYGFG VTLYPNSRES SGYLRLAFHV CSGEN DAIL EWPVENRQVI ITILDQEPDV RNRMSSSMVF TTSKSHTSPA INDTVIWDRP SRVGTYHTDC NCFRSIDLGW SGFISH QML KRRSFLKNDD LIIFVDFEDI THLS |
-Macromolecule #5: N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-ala...
Macromolecule | Name: N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide type: ligand / ID: 5 / Number of copies: 4 / Formula: M6X |
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Molecular weight | Theoretical: 372.372 Da |
Chemical component information | ![]() ChemComp-M6X: |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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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 / Details: Pelco EasyGlow | |||||||||
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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
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: 2366 / Average electron dose: 44.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 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 |