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- EMDB-60562: Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRN... -
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Open data
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Basic information
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Title | Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex B | |||||||||
![]() | Postprocessed by deepEMhancer. | |||||||||
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![]() | RNase / Complex / Contact-dependent growth inhibition / Toxin | |||||||||
Function / homology | ![]() tRNA-specific ribonuclease activity / cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / RNA endonuclease activity / toxin activity / host cell cytoplasm ...tRNA-specific ribonuclease activity / cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / RNA endonuclease activity / toxin activity / host cell cytoplasm / tRNA binding / Hydrolases; Acting on ester bonds / extracellular region / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
![]() | Feng Z / Yashiro Y / Tomita K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system. Authors: Feng Z / Yashiro Y / Tomita K | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 126.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 83 KB | ||
Masks | ![]() | 144.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 134.5 MB 134.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zydMC ![]() 8zycC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Postprocessed by deepEMhancer. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60562_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60562_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CysK in complex with CdiA-CT and tRNA.
Entire | Name: CysK in complex with CdiA-CT and tRNA. |
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Components |
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-Supramolecule #1: CysK in complex with CdiA-CT and tRNA.
Supramolecule | Name: CysK in complex with CdiA-CT and tRNA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Cysteine synthase A
Macromolecule | Name: Cysteine synthase A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cysteine synthase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.756688 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKIFEDNSL TIGHTPLVRL NRIGNGRILA KVESRNPSFS V(LLP)CRIGANMI WDAEKRGVLK PGVELVEPTS GNTGIA LAY VAAARGYKLT LTMPETMSIE RRKLLKALGA NLVLTEGAKG MKGAIQKAEE IVASNPEKYL LLQQFSNPAN PEIHEKT TG PEIWEDTDGQ ...String: MSKIFEDNSL TIGHTPLVRL NRIGNGRILA KVESRNPSFS V(LLP)CRIGANMI WDAEKRGVLK PGVELVEPTS GNTGIA LAY VAAARGYKLT LTMPETMSIE RRKLLKALGA NLVLTEGAKG MKGAIQKAEE IVASNPEKYL LLQQFSNPAN PEIHEKT TG PEIWEDTDGQ VDVFIAGVGT GGTLTGVSRY IKGTKGKTDL ISVAVEPTDS PVIAQALAGE EIKPGPHKIQ GIGAGFIP A NLDLKLVDKV IGITNEEAIS TARRLMEEEG ILAGISSGAA VAAALKLQED ESFTNKNIVV ILPSSGERYL STALFADLF TEKELQQ UniProtKB: Cysteine synthase A |
-Macromolecule #2: tRNA nuclease CdiA
Macromolecule | Name: tRNA nuclease CdiA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.18125 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHVEN NALSLVARGC AVAAPCRTKV AEQLLEIGAK AGMAGLAGAA VKDMADRMTS DELEHLITLQ MMGNDEITTK YLSSLHDKY GSGAASNPNI GKDLTDAEKV ELGGSGSGTG TPPPSENDPK QQNEKTVDKL NQKQESAIKK IDNTIKNALK D HDIIGTLK ...String: MHHHHHHVEN NALSLVARGC AVAAPCRTKV AEQLLEIGAK AGMAGLAGAA VKDMADRMTS DELEHLITLQ MMGNDEITTK YLSSLHDKY GSGAASNPNI GKDLTDAEKV ELGGSGSGTG TPPPSENDPK QQNEKTVDKL NQKQESAIKK IDNTIKNALK D HDIIGTLK DMDGKPVPKE NGGYWDAMQE MQNTLRGLRN HADTLKNVNN PEAQAAYGRA TDAINKIESA LKGYGI UniProtKB: tRNA nuclease CdiA |
-Macromolecule #3: tRNAIleGAU
Macromolecule | Name: tRNAIleGAU / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.000869 KDa |
Sequence | String: AGGCUUGUAG CUCAGGUGGU UAGAGCGCAC CCCUGAU(T6A)AG GGUGAGGUCG GUGGUUCAAG UCCACUCAGG CCUACC A GENBANK: GENBANK: CP053605.1 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.6 mg/mL | |||||||||||||||
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Buffer | pH: 7 Component:
Details: 25mM Tris-HCl,50mM NaCl,2mM MgCl2, 10mM 2-mercaptoethanol | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 7044 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |