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- EMDB-51415: 3D reconstruction of beta-galactosidase obtained from graphene ox... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51415
Title3D reconstruction of beta-galactosidase obtained from graphene oxide modified self-wicking grids
Map data
Sample
  • Organelle or cellular component: Beta-galactosidase
    • Protein or peptide: Beta-Galactosidase
KeywordsHydrolase / glycosidase
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWeckener M / Clare DK / Darrow MC / Naismith JH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Modifying chameleon self-wicking grids with graphene oxide
Authors: Weckener M / Owen CD / Naismith JH / Darrow MC / Clare DK
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_51415.map.gz / Format: CCP4 / Size: 101 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.072 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.11729338 - 0.23166762
Average (Standard dev.)0.00024754138 (±0.006380268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions298298298
Spacing298298298
CellA=B=C: 319.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Beta-galactosidase

EntireName: Beta-galactosidase
Components
  • Organelle or cellular component: Beta-galactosidase
    • Protein or peptide: Beta-Galactosidase

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Supramolecule #1: Beta-galactosidase

SupramoleculeName: Beta-galactosidase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 465 KDa

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Macromolecule #1: Beta-Galactosidase

MacromoleculeName: Beta-Galactosidase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: beta-galactosidase
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MTMITDSLAV VLQRRDWENP GVTQLNRLAA HPPFASWRNS EEARTDRPSQ QLRSLNGEWR FAWFPAPEAV PESWLECDLP EADTVVVPSN WQMHGYDAPI YTNVTYPITV NPPFVPTENP TGCYSLTFNV DESWLQEGQT RIIFDGVNSA FHLWCNGRWV GYGQDSRLPS ...String:
MTMITDSLAV VLQRRDWENP GVTQLNRLAA HPPFASWRNS EEARTDRPSQ QLRSLNGEWR FAWFPAPEAV PESWLECDLP EADTVVVPSN WQMHGYDAPI YTNVTYPITV NPPFVPTENP TGCYSLTFNV DESWLQEGQT RIIFDGVNSA FHLWCNGRWV GYGQDSRLPS EFDLSAFLRA GENRLAVMVL RWSDGSYLED QDMWRMSGIF RDVSLLHKPT TQISDFHVAT RFNDDFSRAV LEAEVQMCGE LRDYLRVTVS LWQGETQVAS GTAPFGGEII DERGGYADRV TLRLNVENPK LWSAEIPNLY RAVVELHTAD GTLIEAEACD VGFREVRIEN GLLLLNGKPL LIRGVNRHEH HPLHGQVMDE QTMVQDILLM KQNNFNAVRC SHYPNHPLWY TLCDRYGLYV VDEANIETHG MVPMNRLTDD PRWLPAMSER VTRMVQRDRN HPSVIIWSLG NESGHGANHD ALYRWIKSVD PSRPVQYEGG GADTTATDII CPMYARVDED QPFPAVPKWS IKKWLSLPGE TRPLILCEYA HAMGNSLGGF AKYWQAFRQY PRLQGGFVWD WVDQSLIKYD ENGNPWSAYG GDFGDTPNDR QFCMNGLVFA DRTPHPALTE AKHQQQFFQF RLSGQTIEVT SEYLFRHSDN ELLHWMVALD GKPLASGEVP LDVAPQGKQL IELPELPQPE SAGQLWLTVR VVQPNATAWS EAGHISAWQQ WRLAENLSVT LPAASHAIPH LTTSEMDFCI ELGNKRWQFN RQSGFLSQMW IGDKKQLLTP LRDQFTRAPL DNDIGVSEAT RIDPNAWVER WKAAGHYQAE AALLQCTADT LADAVLITTA HAWQHQGKTL FISRKTYRID GSGQMAITVD VEVASDTPHP ARIGLNCQLA QVAERVNWLG LGPQENYPDR LTAACFDRWD LPLSDMYTPY VFPSENGLRC GTRELNYGPH QWRGDFQFNI SRYSQQQLME TSHRHLLHAE EGTWLNIDGF HMGIGGDDSW SPSVSAEFQL SAGRYHYQLV WCQK

UniProtKB: Beta-galactosidase

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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

Concentration4.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTrisTris HCl
50.0 mMNaClSodium chloride
1.0 mMTCEPTCEP
2.0 mMMgCl2Magnesium chloride
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 65 sec. / Pretreatment - Atmosphere: AIR
Details: SPT Labtech 300 mesh 1.2/0.8 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were modified with graphene oxide and glow-discharged on at 12 mA ...Details: SPT Labtech 300 mesh 1.2/0.8 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were modified with graphene oxide and glow-discharged on at 12 mA for 65 s to activate the nanowires. Approximately 6 nL of the sample were applied to the grids using a Chameleon system (SPT Labtech) at 62% relative humidity and ambient temperature.
VitrificationCryogen name: ETHANE / Chamber humidity: 62 % / Chamber temperature: 299.95 K / Instrument: SPOTITON
Details: Please update the instrument to SPT Labtech chameleon.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsEPU auto-function coma free correction
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 15331 / Average exposure time: 3.5 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 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: 1983231
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

2984

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 441059
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3

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