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Yorodumi- EMDB-21983: Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21983 | |||||||||||||||||||||||||||||||||||||||
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Title | Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB from Mycobacterium smegmatis | |||||||||||||||||||||||||||||||||||||||
Map data | Density modified map | |||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | Glycosyltransferase / membrane protein / nanodisc | |||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / Transferases; Glycosyltransferases; Pentosyltransferases / cell wall organization / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Tan YZ / Rodrigues J | |||||||||||||||||||||||||||||||||||||||
Funding support | United States, Portugal, European Union, Canada, 12 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Authors: Yong Zi Tan / José Rodrigues / James E Keener / Ruixiang Blake Zheng / Richard Brunton / Brian Kloss / Sabrina I Giacometti / Ana L Rosário / Lei Zhang / Michael Niederweis / Oliver B ...Authors: Yong Zi Tan / José Rodrigues / James E Keener / Ruixiang Blake Zheng / Richard Brunton / Brian Kloss / Sabrina I Giacometti / Ana L Rosário / Lei Zhang / Michael Niederweis / Oliver B Clarke / Todd L Lowary / Michael T Marty / Margarida Archer / Clinton S Potter / Bridget Carragher / Filippo Mancia / Abstract: Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti- ...Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding. | |||||||||||||||||||||||||||||||||||||||
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_21983.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-21983-v30.xml emd-21983.xml | 37.2 KB 37.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21983_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_21983.png | 166.3 KB | ||
Masks | emd_21983_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-21983.cif.gz | 7.6 KB | ||
Others | emd_21983_additional_1.map.gz emd_21983_additional_2.map.gz emd_21983_additional_3.map.gz emd_21983_additional_4.map.gz emd_21983_additional_5.map.gz emd_21983_additional_6.map.gz emd_21983_half_map_1.map.gz emd_21983_half_map_2.map.gz | 18.2 MB 59.6 MB 8.4 MB 7.1 MB 107.1 KB 3.4 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21983 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21983 | HTTPS FTP |
-Related structure data
Related structure data | 6x0oMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10420 (Title: Single-Particle Cryo-EM of Arabinosyltransferase EmbB from Mycobacterium smegmatis, Collected using both Falcon III and K2 Detectors Data size: 4.5 TB Data #1: Unaligned and compressed multiframe movies from Falcon III Detector [micrographs - multiframe] Data #2: Unaligned and compressed multiframe movies from K2 Summit Detector [micrographs - multiframe] Data #3: Aligned and dose-weighted micrographs from Falcon III Detector [micrographs - single frame] Data #4: Aligned and dose-weighted micrographs from K2 Summit Detector [micrographs - single frame] Data #5: Final Particle Stack with Refined Euler Angles and Shifts [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21983.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density modified map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21983_msk_1.map | ||||||||||||
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-Additional map: Raw map
File | emd_21983_additional_1.map | ||||||||||||
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Annotation | Raw map | ||||||||||||
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-Additional map: CryoSPARC Sharpened Map
File | emd_21983_additional_2.map | ||||||||||||
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Annotation | CryoSPARC Sharpened Map | ||||||||||||
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-Additional map: 3DFSC - Raw
File | emd_21983_additional_3.map | ||||||||||||
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Annotation | 3DFSC - Raw | ||||||||||||
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-Additional map: 3DFSC - Thresholded
File | emd_21983_additional_4.map | ||||||||||||
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Annotation | 3DFSC - Thresholded | ||||||||||||
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-Additional map: 3DFSC - Thresholded and binarized
File | emd_21983_additional_5.map | ||||||||||||
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Annotation | 3DFSC - Thresholded and binarized | ||||||||||||
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-Additional map: Local resolution map
File | emd_21983_additional_6.map | ||||||||||||
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Annotation | Local resolution map | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_21983_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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-Half map: Half map 2
File | emd_21983_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Entire | Name: Integral membrane indolylacetylinositol arabinosyltransferase EmbB |
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Components |
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-Supramolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Supramolecule | Name: Integral membrane indolylacetylinositol arabinosyltransferase EmbB type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) |
Molecular weight | Theoretical: 119 KDa |
-Macromolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Macromolecule | Name: Integral membrane indolylacetylinositol arabinosyltransferase EmbB type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: indolylacetylinositol arabinosyltransferase |
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Source (natural) | Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 118.835375 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS ...String: MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS GEDAGKLQRT GYPDPNLRPA IVGVFTDLTG PAPQGLSVSA EIDTRFTTHP TALKLAAMLL AIVSTVIALL AL WRLDRLD GRRMHRLIPT RWRTVTAVDG VVVGGMAIWY VIGANSSDDG YILQMARTAE HAGYMANYFR WFGSPEDPFG WYY NVLALM TKVSDASIWI RLPDLICALI CWLLLSREVL PRLGPAVAGS RAAMWAAGLV LLGAWMPFNN GLRPEGQIAT GALI TYVLI ERAVTSGRLT PAALAITTAA FTLGIQPTGL IAVAALLAGG RPILRIVMRR RRLVGTWPLI APLLAAGTVI LAVVF ADQT IATVLEATRI RTAIGPSQEW WTENLRYYYL ILPTTDGAIS RRVAFVFTAM CLFPSLFMML RRKHIAGVAR GPAWRL MGI IFATMFFLMF TPTKWIHHFG LFAAVGGAMA ALATVLVSPT VLRSARNRMA FLSLVLFVLA FCFASTNGWW YVSNFGA PF NNSVPKVGGV QISAIFFALS AIAALWAFWL HLTRRTESRV VDRLTAAPIP VAAGFMVVVM MASMAIGVVR QYPTYSNG W ANIRAFAGGC GLADDVLVEP DSNAGFLTPL PGAYGPLGPL GGEDPQGFSP DGVPDRIIAE AIRLNNPQPG TDYDWNRPI KLDEPGINGS TVPLPYGLDP KRVPVAGTYS TEAQQESRLS SAWYELPARD ETERAAHPLV VITAAGTITG ESVANGLTTG QTVDLEYAT RGPDGTLVPA GRVTPYDVGP TPSWRNLRYP RSEIPDDAVA VRVVAEDLSL SQGDWIAVTP PRVPELQSVQ E YVGSDQPV LMDWAVGLAF PCQQPMLHAN GVTEVPKFRI SPDYYAKLQS TDTWQDGING GLLGITDLLL RASVMSTYLS QD WGQDWGS LRKFDTVVEA TPAELDFGSQ THSGLYSPGP LRIRPAENLY FQGWSHPQFE K UniProtKB: Integral membrane indolylacetylinositol arabinosyltransferase EmbB |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Macromolecule | Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 3 / Number of copies: 2 / Formula: LHG |
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Molecular weight | Theoretical: 722.97 Da |
Chemical component information | ChemComp-LHG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 278 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Number real images: 2158 / #0 - Average exposure time: 86.4 sec. / #0 - Average electron dose: 78.02 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Digitization - Dimensions - Width: 3838 pixel / #1 - Digitization - Dimensions - Height: 3710 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 7833 / #1 - Average exposure time: 8.0 sec. / #1 - Average electron dose: 77.53 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |