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Yorodumi- EMDB-4906: Cryo-EM reconstruction of TssA protein from T6SS of Escherichia coli. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4906 | |||||||||
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Title | Cryo-EM reconstruction of TssA protein from T6SS of Escherichia coli. | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Type VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Putative type VI secretion protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Nazarov S / Shneider M / Basler M / Leiman P | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of TssA protein from Type VI secretion system of E. coli. Authors: Nazarov S / Demurtas D / Shneider M / Basler M / Leiman P | |||||||||
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_4906.map.gz | 100.6 MB | EMDB map data format | |
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Header (meta data) | emd-4906-v30.xml emd-4906.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4906_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_4906.png | 144 KB | ||
Masks | emd_4906_msk_1.map | 129.7 MB | Mask map | |
Others | emd_4906_additional_1.map.gz emd_4906_additional_2.map.gz emd_4906_half_map_1.map.gz emd_4906_half_map_2.map.gz | 37.8 MB 120.5 MB 95.6 MB 97.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4906 | HTTPS FTP |
-Related structure data
Related structure data | 6rjuMUC M: atomic model generated by this map U: unfit; in different coordinate system*YM C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4906.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.058 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_4906_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_4906_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_4906_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4906_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4906_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C-terminal domain of T6SS protein TssA.
Entire | Name: C-terminal domain of T6SS protein TssA. |
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Components |
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-Supramolecule #1: C-terminal domain of T6SS protein TssA.
Supramolecule | Name: C-terminal domain of T6SS protein TssA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 634 KDa |
-Macromolecule #1: Putative type VI secretion protein
Macromolecule | Name: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 59.159789 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MASIHSLLSA CQTTPRDVAE PAQVRIALWD KWLAPVTPDN PAGDDAGYDD DFQQMREEVN KLSGADAGIV SQLAEKLLTT RTKDIRVAT WYIWARLRQD GEKGLADGLE LLTGLLQRFG EHLHPQRSRA RKAALEWLCS ARILDSLSLY PEVVKADTLR I AGALWLAE ...String: MASIHSLLSA CQTTPRDVAE PAQVRIALWD KWLAPVTPDN PAGDDAGYDD DFQQMREEVN KLSGADAGIV SQLAEKLLTT RTKDIRVAT WYIWARLRQD GEKGLADGLE LLTGLLQRFG EHLHPQRSRA RKAALEWLCS ARILDSLSLY PEVVKADTLR I AGALWLAE QTFTDEASAP VLNGLYQALE NRLMKAGGVD AVVPQEAAAP APTVTSGSVM ALSAITSGQE LLSQARVLAK YL RDQPEGW LAAHRLMKSV RHDTLHQLPP LSADGRTRIA PPGPDRRASL KRLYLQQNWL SLLEQCDDMF ARGASHLWLD LQW YIHQAL LQTGKENYAA IIQYDLKGLL LRLPGLETLA FNDGMPFADD VTLSWIQQQV MECGERWAEE PSVTITAAPG DNDI LSLEP EALQIADNEG TEAALSWLQA RPGIQSDRSN WLLRLL(MSE)ARV AEQTGKNDLA LHLLAELDER ATRLTLSQWE P ELVFEVKA RRLKLLR(MSE)KS AKTESDRVRL QPD(MSE)EHLLAG LIAIDAARAA VLCNSGSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2. |
-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 |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3269 / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |