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- EMDB-72225: Cryo EM structure of alpha-glucosidase (yicI) from Klebsiella aer... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72225
TitleCryo EM structure of alpha-glucosidase (yicI) from Klebsiella aerogenes
Map dataMain map
Sample
  • Organelle or cellular component: alpha-glucosidase
    • Protein or peptide: Alpha-glucosidase yicI
KeywordsSSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / alpha-glucosidase / Klebsiella aerogenes / HYDROLASE
Function / homology
Function and homology information


alpha-D-xyloside xylohydrolase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-xyloside xylohydrolase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLovell S / Liu L / Ingham DJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Cryo EM structure of alpha-glucosidase (yicI) from Klebsiella aerogenes
Authors: Liu L / Lovell S / Ingham DJ
History
DepositionAug 20, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72225.png

Downloads & links

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Map

FileDownload / File: emd_72225.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 420 pix.
= 226.8 Å		0.54 Å/pix.
x 420 pix.
= 226.8 Å		0.54 Å/pix.
x 420 pix.
= 226.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.022642199 - 0.06902751
Average (Standard dev.)0.0014577509 (±0.0051320163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 226.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72225_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72225_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha-glucosidase

EntireName: alpha-glucosidase
Components
  • Organelle or cellular component: alpha-glucosidase
    • Protein or peptide: Alpha-glucosidase yicI

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Supramolecule #1: alpha-glucosidase

SupramoleculeName: alpha-glucosidase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella aerogenes KCTC 2190 (bacteria)
Molecular weightTheoretical: 531.87 KDa

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Macromolecule #1: Alpha-glucosidase yicI

MacromoleculeName: Alpha-glucosidase yicI / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella aerogenes KCTC 2190 (bacteria)
Molecular weightTheoretical: 88.650727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHMK ISDGNWLIQP GLNLIQPVQV YEVEQQGNEM VVYAAPRDVR ERAWQLDTPL FTLRFFSPQE GIIGVRMEHF QGALDNSPH YPLNVQKDVH VEIENTAEFA ELKSGSLSVR VTKGEFWALD FLRDGVRITG SQLKNNGYVQ DSKTQRNYMF E RLDLGVGE ...String:
MAHHHHHHMK ISDGNWLIQP GLNLIQPVQV YEVEQQGNEM VVYAAPRDVR ERAWQLDTPL FTLRFFSPQE GIIGVRMEHF QGALDNSPH YPLNVQKDVH VEIENTAEFA ELKSGSLSVR VTKGEFWALD FLRDGVRITG SQLKNNGYVQ DSKTQRNYMF E RLDLGVGE TVYGLGERFT ALVRNGQTVE TWNEDGGTST EQSYKNIPFY LTNRGYGVLV NHPQRVSFEV GSEKVSKVQF SV EGEYLEY FVIDGPTPKA VLNRYTQFTG RPALPPAWSF GLWLTTSFTT NYDEATVNSF IDGMAERHLP LHVFHFDCFW MKA FQWCDF EWDPLTFPDP EGMIKRLKAK GLKVCVWINP YIGQRSPVFK ELKEKGYLLK RPDGSLWQWD KWQPGLAIYD FTNP EACQW YASKLKGLVA MGVDCFKTDF GERIPTDVQW FDGSDPQKMH NHYAFIYNEL VWKVLKETVG EQEAVLFARS ASVGA QQFP VHWGGDCYAN YESMAESLRG GLSIGMSGFG FWSHDIGGFE NTAPAHVYKR WCAFGLLSSH SRLHGSKSYR VPWAYD EES CDVVRHFTQL KCRMMPYLYR QAALANEFGT PMLRAMMLEF PDDPACDYLD RQYMLGDSVL VAPVFSEAGE VQFYLPE GR WTHLWHNDEL PGSRWHKQRH DALSLPVYVR DNTLLALGNN DQKPDYAWHE GTAFQLFQLG DGNETVCQVP AADGSAIF T LKAKRQGNTI TVSGEGEARG WTLCLRNIPQ IAGVEGGTQA GSELGVVVSA QGNALTISL

UniProtKB: alpha-D-xyloside xylohydrolase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration2.09 mg/mL
BufferpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Pressure: 0.005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 60.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Cs: 2.7 mm / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 925341
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8t7z

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 153600
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8t7z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9q5c:
Cryo EM structure of alpha-glucosidase (yicI) from Klebsiella aerogenes

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