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Yorodumi- EMDB-26481: Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26481 | |||||||||
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Title | Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A | |||||||||
Map data | bl1327 mut mannose 2.71 A | |||||||||
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 / oligosaccharide catabolic process / fungal-type vacuole membrane / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bifidobacterium longum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 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_Man38A nucleophile mutant in complex with mannose at 2.7 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_26481.map.gz | 676.6 MB | EMDB map data format | |
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Header (meta data) | emd-26481-v30.xml emd-26481.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_26481.png | 90.4 KB | ||
Filedesc metadata | emd-26481.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26481 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26481 | HTTPS FTP |
-Related structure data
Related structure data | 7ufuMC 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_26481.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | bl1327 mut mannose 2.71 A | ||||||||||||||||||||
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 nucleophile mutant version of Bl1_Man38A in complex w...
Entire | Name: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose |
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Components |
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-Supramolecule #1: Tetramer of nucleophile mutant version of Bl1_Man38A in complex w...
Supramolecule | Name: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bifidobacterium longum (bacteria) |
Molecular weight | Theoretical: 471 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: 117.943125 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMFLKPEQ QLERCRRIVR QRVDPHIHPS IAQLTVESYD IPGEPMPSDE FFAKLDRGDI DFKPFMLGS EWGTTWGTVW FRLTGTVPAG YPKGKPLELI LDLGWYPHSC GGHIEGLVYR ADGTAIKAVH PLNYWVPFMD A EGNAQVPV ...String: MGSSHHHHHH SSGLVPRGSH MASMFLKPEQ QLERCRRIVR QRVDPHIHPS IAQLTVESYD IPGEPMPSDE FFAKLDRGDI DFKPFMLGS EWGTTWGTVW FRLTGTVPAG YPKGKPLELI LDLGWYPHSC GGHIEGLVYR ADGTAIKAVH PLNYWVPFMD A EGNAQVPV AEDGSFTLYL EAASNPLLLG VPPFIETELG DHATGKPDEP YVFKSADLAE FDERYENYSV DLDVVSSLME FA DKQSPRY WQLAKALQRS LNAYDERNPE SVEAARAVLA GVLAKPANAS AMNVSAIGHA HIDSAWLWPV RETRRKVART VSN ALALMD ADPDFKYAMS SAQQYAWLEE DHPDIFKRMK RRIEEGRFIP VGGMWVEADG MLPAGESLIR QIAYGRKYFK EHLG VEPKG VWLPASFGYT GAWPQIARRA GYEWFLTQKI SWNDTTKFPH HSFMWEGIDG SRIFTHFPPA DTYAAWCKVQ ELDYA EKNF QDKDLSDRSL LLFGFGDGGG GPTRNMMEHL HRYENLEGVS KVSIEEPNDF FDKAHQQLAE NAGPEMPVWK GELYLE LHR GTLTSQQDMK RGCRQEESLL RTVEYLGAAA VLSDPEYVYP REELDRIWKT LLLNQFHDIL PGSAIAWVHR EAREDYR RD LKRLAEIAQD MCAVLRKANP QADLLAEARI SQFRNDGASW HANRINEPTD ALSVLTQTLD NGRVLLANGV LSVTIEAD G TISSLLDEEH GRELVPAGTR LGQYELLRDE PAVWDAWEIE RESLLMANAV TGSIESVNTE NGAAQVHVHT ADGDTVITT TITLRPGSHT LDFHADIDWH ERERFLKVDL PLGIVADQAT YDCQYGLIRR PIVKNTASDE AKYESSTNRF AIIGDAGYAA AVINGSVYG SDASPIAGNA AEGRDSGTMF RLSLLSAPTF PDPRTDIGSH EFDWSVVADA TVDRALDAAG VLNAPVLHDV P DITPLASI ESVNGTVVLD WMKLADDGSG DLIVRAYEAA GGQADAMLHV CPALAGASVH ETNVLEGDDL AADLPVALQD GR QNAEGAT LHFGPFQLAT LRITR 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 |
-Macromolecule #3: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.2 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 R2/2 / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 16231 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM |