+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26480 | |||||||||
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Title | Cryo-EM Structure of Bl_Man38C at 2.9 A | |||||||||
Map data | ||||||||||
Sample |
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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: 2.9 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_Man38C at 2.9 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_26480.map.gz | 676.7 MB | EMDB map data format | |
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Header (meta data) | emd-26480-v30.xml emd-26480.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_26480.png | 92.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26480 | HTTPS FTP |
-Related structure data
Related structure data | 7uftMC 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_26480.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_Man38C
Entire | Name: Tetramer of Bl_Man38C |
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Components |
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-Supramolecule #1: Tetramer of Bl_Man38C
Supramolecule | Name: Tetramer of Bl_Man38C / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bifidobacterium longum (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 470 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: 117.651789 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMLLKVNR EIDRCKRVMR ERVWPHIHQV LAQCTVGAVK NPGEPEMPAA FITRAVSGQV IFQPLAVGE PWGTSWGTTW IRVEGQLPET LPEGRAIELV FNLGWLEWPV GGHIEAMAYR ADGTVIKALH PRNHWMPLVS A DGVKDRVV ...String: MGSSHHHHHH SSGLVPRGSH MASMLLKVNR EIDRCKRVMR ERVWPHIHQV LAQCTVGAVK NPGEPEMPAA FITRAVSGQV IFQPLAVGE PWGTSWGTTW IRVEGQLPET LPEGRAIELV FNLGWLEWPV GGHIEAMAYR ADGTVIKALH PRNHWMPLVS A DGVKDRVV NPDGSFVVYV EGAYNPNVPS FTVTELGTKP TGKADERYEF SSIDIAALDQ DMFDYWADLD VVTGSLENMN DA DPRYWKL AKAMQRSINL WDEKDYNTLA LARKALDKVM HNPANASAMT LTAMGHSHID SAWLWPVRET ERKVGRTVSN ALA LMDIDP DFTYVMSAAQ HFAWLEERHP DLFERVKARI AEGRFIPVGG MWVESDGTMP CGESLIRQIS YGKRYFKEKL GVVP NGIWL PDSFGYTGAW PQIAKRSGYS WFLTQKLCWN DTTRLPHHSF MWEGVDGSQI FTHFPPADKY DSDMSANDMA YVQSN YKDK DLSDRGILLF GYGDGGGGPI REMTMREHRF ESFEGMPKVE YGTPDDFFSK AETEMKAEAG SEMPRWKGEF YFELHR KTL TSQQEMKRGC RKEESMLRTV EYLGVVASLE SADYVYPTER IDRIWKTLLL SQFHDILPGS AIEWAHRVAR EEYARDL KA LSDIARDAIA AIAVANPDVA RIAKARISQF ADVDPWRPAS LVSCGEPVEV NRREDGSATL DNGLLCVHVA ADGTVDSM I DLKSGREMVA KDHVMGRYEI LKDEPGVFDA WDVERDAFLC ATALADGHIV SIETTADGSA VIVTKNSYRD DEISTTITL RPGKSQLDFH ADVEWNVPEK LLKVDIPMAL SASRAQYECQ YGLIERPIVK NTEGEEAMFE SCSHRFVRIH DSSYGIGVAN GSTYGSDVS SLRDRDDALA GTMVRMSLVA APTAPDPRTD IGHHEFDWTV LPCASVAPLV AAAGEINAPT IENMPDIAAP I TLEPIEGT PVIDWIKLAD DGSGDIVARL YEAAGAKAKA MLHVGGTLDG WTVRETNTLE QDESYPDEPA GLIGGKQQAE GA ELALNPF QLTTLRLSRA |
-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 | 0.34 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 |
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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: cisTEM |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM |
Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 56677 |