+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26479 | |||||||||
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Title | Cryo-EM Structure of Bl_Man38B at 3.4 A | |||||||||
Map data | ||||||||||
Sample |
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Keywords | n-glycan / probiotic / a-mannosidase / gh38 / HYDROLASE | |||||||||
Function / homology | Function and homology information alpha-mannosidase activity / mannose metabolic process / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bifidobacterium longum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Santos CR / Cordeiro RL / Domingues MN / Borges AC / de Farias MA / Van Heel M / Murakami MT / Portugal RV | |||||||||
Funding support | Brazil, 2 items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Cryo-EM Structure of Bl_Man38B at 3.4 A Authors: Santos CR / Cordeiro RL / Domingues MN / Borges AC / de Farias MA / Van Heel M / Murakami MT / Portugal RV | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26479.map.gz | 676.8 MB | EMDB map data format | |
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Header (meta data) | emd-26479-v30.xml emd-26479.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_26479.png | 89.5 KB | ||
Filedesc metadata | emd-26479.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26479 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26479 | HTTPS FTP |
-Validation report
Summary document | emd_26479_validation.pdf.gz | 667.2 KB | Display | EMDB validaton report |
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Full document | emd_26479_full_validation.pdf.gz | 666.8 KB | Display | |
Data in XML | emd_26479_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_26479_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26479 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26479 | HTTPS FTP |
-Related structure data
Related structure data | 7ufsMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26479.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Tetramer of Bl_Man38B
Entire | Name: Tetramer of Bl_Man38B |
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Components |
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-Supramolecule #1: Tetramer of Bl_Man38B
Supramolecule | Name: Tetramer of Bl_Man38B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bifidobacterium longum (bacteria) |
Molecular weight | Theoretical: 475 KDa |
-Macromolecule #1: Alpha-mannosidase
Macromolecule | Name: Alpha-mannosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bifidobacterium longum (bacteria) / Strain: NCC 2705 |
Molecular weight | Theoretical: 118.789016 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMFLLPNQ QLERCDRVMQ QRVKPHIHTT LAACTLRSFH NPGEPVPSSE FLAKVRNGQV PFEPFRVPG VWGTTWGTTW FEVNGHIDMA AVKGRKVELM VDLGWLDHRG PGFQSEGLVY RADGTAIKSA NPRNHWIPLV Y ADGSSTVE ...String: MGSSHHHHHH SSGLVPRGSH MASMFLLPNQ QLERCDRVMQ QRVKPHIHTT LAACTLRSFH NPGEPVPSSE FLAKVRNGQV PFEPFRVPG VWGTTWGTTW FEVNGHIDMA AVKGRKVELM VDLGWLDHRG PGFQSEGLVY RADGTAIKSA NPRNHWIPLV Y ADGSSTVE LDEHGDFTVY IEAAANPFVE GPTPFSPTEL GEEATGTCDF PYTLSRMDIT IFNEDVFAYD MDLETVSSLI RE LKDDDPR YWQLAKALQR SLNIYDERDL ETVPAARAAL AGVLAEPAAS SAINHIAIGH AHIDSAWLWP VRETRRKVAR TVS NVLALM DEDPDFTYAM SSAQQYAWLE EEHPDLFARM KRRIEEGRFI PVGGMWVESD NMIPSGESLV RQITFGRRYF KEHL GVTPR GIWLPDSFGY AGSWPQIARR AGFDWFLTQK ISWNDTTKFP HHSFMWEGID GTRILTHFPP SDTYCSSMSM RELMY SQRN FLDKDLSRNA ILLYGFGDGG GGPTREMTAR IRRDHDLAGA PKIDFGTPDQ LFDRVRKDIV DDARGETPVF HGELYL ELH RGTLTAQQDM KRGCRQEESM LRVVEYLCAV ASIKNPGYVY PREELDRIWK TLLLNQFHDI LPGSAIAWVH RQAREEY AR DIAHLRDIAA AAGQAVKEAE PGIATVKHAV IAPYASNPQY SWAVRDGGGT AVEESVIPVS VERGGNAIIL DNGRLRVR I EADGTVSSLI DLALRRELVP SGVRMGRYEL LKDEPFHWDA WDIQRDAFLA ADTLTDAMVE HVEDMPDGSA AIHVVTRAR GVEIHTVITL RPGSGSLDFT ADVNWHAVEK FLKVDMPVTV QAVNAQYECQ YGLVERPINK NTRSDDAKFE SCTHRFVRIA DADYAAAVV NASTYGSDVS PIHAAAAHGA GRGTMVRLSL LSAPLYPDPR TDQGEHFFAW SLVAGAGMES VLAEASRLNA P IMGELPAV RPLATLTDVA GTPVLDWVKL ADDGSGDLIV RLYEAAGGDA KATLRLDDTF AGCTVEEVNL MEEPVLADDL PR ALVAGGP VPAEGASVSF TPFQIVTLRI RR UniProtKB: Alpha-mannosidase |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.783 mg/mL |
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Buffer | pH: 7.5 Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
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
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 7865 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM |