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- EMDB-26479: Cryo-EM Structure of Bl_Man38B at 3.4 A -

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Basic information

Entry
Database: EMDB / ID: EMD-26479
TitleCryo-EM Structure of Bl_Man38B at 3.4 A
Map data
Sample
  • Complex: Tetramer of Bl_Man38B
    • Protein or peptide: Alpha-mannosidase
  • Ligand: ZINC ION
Keywordsn-glycan / probiotic / a-mannosidase / gh38 / HYDROLASE
Function / homology
Function and homology information


alpha-mannosidase activity / mannose metabolic process / oligosaccharide catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain ...Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
Biological speciesBifidobacterium longum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSantos CR / Cordeiro RL / Domingues MN / Borges AC / de Farias MA / Van Heel M / Murakami MT / Portugal RV
Funding support Brazil, 2 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
CitationJournal: 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
DepositionMar 23, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26479.png

Downloads & links

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Map

FileDownload / File: emd_26479.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 576 pix.
= 385.92 Å		0.67 Å/pix.
x 576 pix.
= 385.92 Å		0.67 Å/pix.
x 576 pix.
= 385.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-11.723635 - 21.029724000000002
Average (Standard dev.)-0.00017356026 (±0.88862747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 385.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tetramer of Bl_Man38B

EntireName: Tetramer of Bl_Man38B
Components
  • Complex: Tetramer of Bl_Man38B
    • Protein or peptide: Alpha-mannosidase
  • Ligand: ZINC ION

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Supramolecule #1: Tetramer of Bl_Man38B

SupramoleculeName: Tetramer of Bl_Man38B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bifidobacterium longum (bacteria)
Molecular weightTheoretical: 475 KDa

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Macromolecule #1: Alpha-mannosidase

MacromoleculeName: Alpha-mannosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bifidobacterium longum (bacteria) / Strain: NCC 2705
Molecular weightTheoretical: 118.789016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.783 mg/mL
BufferpH: 7.5
Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5
GridModel: 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied 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 assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM

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