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- EMDB-26481: Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-26481
TitleCryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A
Map databl1327 mut mannose 2.71 A
Sample
  • Complex: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose
    • Protein or peptide: Alpha-mannosidase
  • Ligand: ZINC ION
  • Ligand: alpha-D-mannopyranose
Function / homology
Function and homology information


alpha-mannosidase activity / mannose metabolic 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 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central 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: 2.7 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_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
DepositionMar 23, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26481.png

Downloads & links

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Map

FileDownload / File: emd_26481.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbl1327 mut mannose 2.71 A
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: 4.5
Minimum - Maximum-18.032276 - 31.28796
Average (Standard dev.)-0.00087562244 (±1.2528614)
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 nucleophile mutant version of Bl1_Man38A in complex w...

EntireName: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose
Components
  • Complex: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose
    • Protein or peptide: Alpha-mannosidase
  • Ligand: ZINC ION
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Tetramer of nucleophile mutant version of Bl1_Man38A in complex w...

SupramoleculeName: Tetramer of nucleophile mutant version of Bl1_Man38A in complex with mannose
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bifidobacterium longum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 471 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: 117.943125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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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Macromolecule #3: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

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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

Concentration2.2 mg/mL
BufferpH: 7.5
Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

CTF correctionSoftware - Name: cisTEM
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final reconstructionApplied 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

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