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Yorodumi- EMDB-26424: Meprin alpha helix in complex with fetuin-B [consensus C1 reconst... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26424 | |||||||||
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Title | Meprin alpha helix in complex with fetuin-B [consensus C1 reconstruction] | |||||||||
Map data | B-factor amplitude corrected sharpened map, filtered by local resolution | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 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_26424.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-26424-v30.xml emd-26424.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26424_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_26424.png | 108.3 KB | ||
Masks | emd_26424_msk_1.map | 103 MB | Mask map | |
Others | emd_26424_additional_1.map.gz emd_26424_half_map_1.map.gz emd_26424_half_map_2.map.gz | 51.8 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26424 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26424 | HTTPS FTP |
-Validation report
Summary document | emd_26424_validation.pdf.gz | 918 KB | Display | EMDB validaton report |
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Full document | emd_26424_full_validation.pdf.gz | 917.6 KB | Display | |
Data in XML | emd_26424_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_26424_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26424 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26424 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26424.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | B-factor amplitude corrected sharpened map, filtered by local resolution | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4133 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26424_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened final map. Low pass filtered to the global FSC.
File | emd_26424_additional_1.map | ||||||||||||
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Annotation | Unsharpened final map. Low pass filtered to the global FSC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map (1 of 2).
File | emd_26424_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_26424_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 : Inhibitory complex of meprin alpha helix with fetuin-B [consensus...
Entire | Name: Inhibitory complex of meprin alpha helix with fetuin-B [consensus C1 reconstruction] |
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Components |
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-Supramolecule #1: Inhibitory complex of meprin alpha helix with fetuin-B [consensus...
Supramolecule | Name: Inhibitory complex of meprin alpha helix with fetuin-B [consensus C1 reconstruction] type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all Details: Consensus standard reconstruction of full helix of recombinant, secreted helical pro-meprin alpha |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Drosophila (fruit flies) / Recombinant cell: Schneider-2 / Recombinant plasmid: pMT/BiP/V5 |
Molecular weight | Theoretical: 85 kDa/nm |
-Macromolecule #1: Meprin alpha
Macromolecule | Name: Meprin alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDIL LQ KSRNGLRDPN TRWTFPIPYI LADNLGLNAK GAILYAFEMF RLKSCVDFKP YEGESSYI I FQQFDGCWSE VGDQHVGQNI SIGQGCAYKA IIEHEILHAL GFYHEQSRTD RDDYVNIWW ...String: WSHPQFEKVP IKYLPEENVH DADFGEQKDI SEINLAAGLD LFQGDIL LQ KSRNGLRDPN TRWTFPIPYI LADNLGLNAK GAILYAFEMF RLKSCVDFKP YEGESSYI I FQQFDGCWSE VGDQHVGQNI SIGQGCAYKA IIEHEILHAL GFYHEQSRTD RDDYVNIWW DQILSGYQHN FDTYDDSLIT DLNTPYDYES LMHYQPFSFN KNASVPTITA KIPEFNSIIG QRLDFSAID LERLNRMYNC TTTHTLLDHC TFEKANICGM IQGTRDDTDW AHQDSAQAGE V DHTLLGQC TGAGYFMQFS TSSGSAEEAA LLESRILYPK RKQQCLQFFY KMTGSPSDRL VV WVRRDDS TGNVRKLVKV QTFQGDDDHN WKIAHVVLKE EQKFRYLFQG TKGDPQNSTG GIY LDDITL TETPCPTGVW TVRNFSQVLE NTSKGDKLQS PRFYNSEGYG FGVTLYPNSR ESSG YLRLA FHVCSGENDA ILEWPVENRQ VIITILDQEP DVRNRMSSSM VFTTSKSHTS PAIND TVIW DRPSRVGTYH TDCNCFRSID LGWSGFISHQ MLKRRSFLKN DDLIIFVDFE DITHLS |
-Macromolecule #2: fetuin-B
Macromolecule | Name: fetuin-B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGLLLPLALC ILVLCCGAMS PPQLALNPSA LLSRGCNDSD VLAVAGFALR DINKDRKDGY VLRLNRVND AQEYRRGGLG SLFYLTLDVL ETDCHVLRKK AWQDCGMRIF FESVYGQCKA I FYMNNPSR VLYLAAYNCT LRPVSKKKIY MTCPDCPSSI PTDSSNHQVL ...String: MGLLLPLALC ILVLCCGAMS PPQLALNPSA LLSRGCNDSD VLAVAGFALR DINKDRKDGY VLRLNRVND AQEYRRGGLG SLFYLTLDVL ETDCHVLRKK AWQDCGMRIF FESVYGQCKA I FYMNNPSR VLYLAAYNCT LRPVSKKKIY MTCPDCPSSI PTDSSNHQVL EAATESLAKY NN ENTSKQY SLFKVTRASS QWVVGPSYFV EYLIKESPCT KSQASSCSLQ SSDSVPVGLC KGS LTRTHW EKFVSVTCDF FESQAPATGS ENSAVNQKPT NLPKVEESQQ KNTPPTDSPS KAGP RGSVQ YLPDLDDKNS QEKGPQEAFP VHLDLTTNPQ GETLDISFLF LEPMEEKLVV LPFPK EKAR TAECPGPAQN ASPLVLPPHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.0 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 4068 / 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: 2.0 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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Refinement | Space: REAL / Protocol: RIGID BODY FIT |