+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10563 | |||||||||
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Title | Beta-galactosidase in complex with deoxygalacto-nojirimycin | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | Bgal / nojirimycin / SUGAR BINDING PROTEIN | |||||||||
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 | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Saur M / Hartshorn MJ | |||||||||
Citation | Journal: Drug Discov Today / Year: 2020 Title: Fragment-based drug discovery using cryo-EM. Authors: Michael Saur / Michael J Hartshorn / Jing Dong / Judith Reeks / Gabor Bunkoczi / Harren Jhoti / Pamela A Williams / Abstract: Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. ...Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-based drug discovery (FBDD) based on in-house method development. We demonstrate not only that cryo-EM can reveal details of the molecular interactions between fragments and a protein, but also that the current reproducibility, quality, and throughput are compatible with FBDD. We exemplify this using the test system β-galactosidase (Bgal) and the oncology target pyruvate kinase 2 (PKM2). | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10563.map.gz | 14.9 MB | EMDB map data format | |
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Header (meta data) | emd-10563-v30.xml emd-10563.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_10563.png | 161.2 KB | ||
Filedesc metadata | emd-10563.cif.gz | 6.2 KB | ||
Others | emd_10563_additional.map.gz emd_10563_additional_1.map.gz emd_10563_half_map_1.map.gz emd_10563_half_map_2.map.gz | 308.9 MB 308.9 MB 261 MB 261.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10563 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10563 | HTTPS FTP |
-Validation report
Summary document | emd_10563_validation.pdf.gz | 396.6 KB | Display | EMDB validaton report |
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Full document | emd_10563_full_validation.pdf.gz | 395.7 KB | Display | |
Data in XML | emd_10563_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10563 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10563 | HTTPS FTP |
-Related structure data
Related structure data | 6tshMC 6tskC 6tteC 6ttfC 6tthC 6ttiC 6ttqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10645 (Title: Beta-galactosidase in complex with deoxygalacto-nojirimycin Data size: 765.8 Data #1: Data from EPU (movies have been converted to compressed TIF) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10563.map.gz / Format: CCP4 / Size: 329.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Relion post-process unmasked map.
File | emd_10563_additional.map | ||||||||||||
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Annotation | Relion post-process unmasked map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Relion post-process unmasked map.
File | emd_10563_additional_1.map | ||||||||||||
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Annotation | Relion post-process unmasked map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion auto-refine halfmap 2
File | emd_10563_half_map_1.map | ||||||||||||
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Annotation | Relion auto-refine halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion auto-refine halfmap 1
File | emd_10563_half_map_2.map | ||||||||||||
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Annotation | Relion auto-refine halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Beta-galactosidase
Entire | Name: Beta-galactosidase |
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Components |
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-Supramolecule #1: Beta-galactosidase
Supramolecule | Name: Beta-galactosidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 464 KDa |
-Macromolecule #1: Beta-galactosidase
Macromolecule | Name: Beta-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: beta-galactosidase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 118.395336 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MLEDPVVLQR RDWENPGVTQ LNRLAAHPPF ASWRNSEEAR TDRPSQQLRS LNGEWRFAWF PAPEAVPES WLECDLPEAD TVVVPSNWQM HGYDAPIYTN VTYPITVNPP FVPTENPTGC YSLTFNVDES WLQEGQTRII F DGVNSAFH ...String: MGSSHHHHHH SSGLVPRGSH MLEDPVVLQR RDWENPGVTQ LNRLAAHPPF ASWRNSEEAR TDRPSQQLRS LNGEWRFAWF PAPEAVPES WLECDLPEAD TVVVPSNWQM HGYDAPIYTN VTYPITVNPP FVPTENPTGC YSLTFNVDES WLQEGQTRII F DGVNSAFH LWCNGRWVGY GQDSRLPSEF DLSAFLRAGE NRLAVMVLRW SDGSYLEDQD MWRMSGIFRD VSLLHKPTTQ IS DFHVATR FNDDFSRAVL EAEVQMCGEL RDYLRVTVSL WQGETQVASG TAPFGGEIID ERGGYADRVT LRLNVENPKL WSA EIPNLY RAVVELHTAD GTLIEAEACD VGFREVRIEN GLLLLNGKPL LIRGVNRHEH HPLHGQVMDE QTMVQDILLM KQNN FNAVR CSHYPNHPLW YTLCDRYGLY VVDEANIETH GMVPMNRLTD DPRWLPAMSE RVTRMVQRDR NHPSVIIWSL GNESG HGAN HDALYRWIKS VDPSRPVQYE GGGADTTATD IICPMYARVD EDQPFPAVPK WSIKKWLSLP GETRPLILCE YAHAMG NSL GGFAKYWQAF RQYPRLQGGF VWDWVDQSLI KYDENGNPWS AYGGDFGDTP NDRQFCMNGL VFADRTPHPA LTEAKHQ QQ FFQFRLSGQT IEVTSEYLFR HSDNELLHWM VALDGKPLAS GEVPLDVAPQ GKQLIELPEL PQPESAGQLW LTVRVVQP N ATAWSEAGHI SAWQQWRLAE NLSVTLPAAS HAIPHLTTSE MDFCIELGNK RWQFNRQSGF LSQMWIGDKK QLLTPLRDQ FTRAPLDNDI GVSEATRIDP NAWVERWKAA GHYQAEAALL QCTADTLADA VLITTAHAWQ HQGKTLFISR KTYRIDGSGQ MAITVDVEV ASDTPHPARI GLNCQLAQVA ERVNWLGLGP QENYPDRLTA ACFDRWDLPL SDMYTPYVFP SENGLRCGTR E LNYGPHQW RGDFQFNISR YSQQQLMETS HRHLLHAEEG TWLNIDGFHM GIGGDDSWSP SVSAEFQLSA GRYHYQLVWC QK UniProtKB: Beta-galactosidase |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
Macromolecule | Name: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / type: ligand / ID: 3 / Number of copies: 4 / Formula: DGJ |
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Molecular weight | Theoretical: 163.172 Da |
Chemical component information | ChemComp-DGJ: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 864 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.17 mg/mL |
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Buffer | pH: 6.8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / 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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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 476 / Number real images: 476 / Average exposure time: 59.98 sec. / Average electron dose: 59.69 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |