+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12353 | |||||||||
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Title | Wzc-K540M-4YE C1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Wzc / regulator / capsular polysaccharide synthesis and transport / Gram-negative pathogens / CARBOHYDRATE | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
Authors | Naismith JH / Liu JW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: The molecular basis of regulation of bacterial capsule assembly by Wzc. Authors: Yun Yang / Jiwei Liu / Bradley R Clarke / Laura Seidel / Jani R Bolla / Philip N Ward / Peijun Zhang / Carol V Robinson / Chris Whitfield / James H Naismith / Abstract: Bacterial extracellular polysaccharides (EPSs) play critical roles in virulence. Many bacteria assemble EPSs via a multi-protein "Wzx-Wzy" system, involving glycan polymerization at the outer face of ...Bacterial extracellular polysaccharides (EPSs) play critical roles in virulence. Many bacteria assemble EPSs via a multi-protein "Wzx-Wzy" system, involving glycan polymerization at the outer face of the cytoplasmic/inner membrane. Gram-negative species couple polymerization with translocation across the periplasm and outer membrane and the master regulator of the system is the tyrosine autokinase, Wzc. This near atomic cryo-EM structure of dephosphorylated Wzc from E. coli shows an octameric assembly with a large central cavity formed by transmembrane helices. The tyrosine autokinase domain forms the cytoplasm region, while the periplasmic region contains small folded motifs and helical bundles. The helical bundles are essential for function, most likely through interaction with the outer membrane translocon, Wza. Autophosphorylation of the tyrosine-rich C-terminus of Wzc results in disassembly of the octamer into multiply phosphorylated monomers. We propose that the cycling between phosphorylated monomer and dephosphorylated octamer regulates glycan polymerization and translocation. | |||||||||
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_12353.map.gz | 18 MB | EMDB map data format | |
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Header (meta data) | emd-12353-v30.xml emd-12353.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_12353.png | 94.6 KB | ||
Filedesc metadata | emd-12353.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12353 | HTTPS FTP |
-Validation report
Summary document | emd_12353_validation.pdf.gz | 402 KB | Display | EMDB validaton report |
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Full document | emd_12353_full_validation.pdf.gz | 401.5 KB | Display | |
Data in XML | emd_12353_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_12353_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12353 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12353 | HTTPS FTP |
-Related structure data
Related structure data | 7nibMC 7nhrC 7nhsC 7ni2C 7nihC 7niiC M: atomic model generated by this map 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_12353.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Octameric complex of Wzc-K540M-4YE
Entire | Name: Octameric complex of Wzc-K540M-4YE |
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Components |
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-Supramolecule #1: Octameric complex of Wzc-K540M-4YE
Supramolecule | Name: Octameric complex of Wzc-K540M-4YE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 640 KDa |
-Macromolecule #1: Tyrosine-protein kinase
Macromolecule | Name: Tyrosine-protein kinase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: non-specific protein-tyrosine kinase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 80.435109 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTSVTSKQST ILGSDEIDLG RVIGELIDHR KLIISITSVF TLFAILYALL ATPIYETDAL IQIEQKQGNA ILSSLSQVLP DGQPQSAPE TALLQSRMIL GKTIDDLNLQ IQIEQKYFPV IGRGLARLMG EKPGNIDITR LYLPDSDDIS NNTPSIILTV K DKENYSIN ...String: MTSVTSKQST ILGSDEIDLG RVIGELIDHR KLIISITSVF TLFAILYALL ATPIYETDAL IQIEQKQGNA ILSSLSQVLP DGQPQSAPE TALLQSRMIL GKTIDDLNLQ IQIEQKYFPV IGRGLARLMG EKPGNIDITR LYLPDSDDIS NNTPSIILTV K DKENYSIN SDGIQLNGVV GTLLNEKGIS LLVNEIDAKP GDQFVITQLP RLKAISDLLK SFSVADLGKD TGMLTLTLTG DN PKRISHI LDSISQNYLA QNIARQAAQD AKSLEFLNQQ LPKVRAELDS AEDKLNAYRK QKDSVDLNME AKSVLDQIVN VDN QLNELT FREAEVSQLY TKEHPTYKAL MEKRQTLQEE KSKLNKRVSS MPSTQQEVLR LSRDVESGRA VYLQLLNRQQ ELNI AKSSA IGNVRIIDNA VTDPNPVRPK KTIIIVIGVV LGLIVSVVLV LFQVFLRRGI ESPEQLEEIG INVYASIPIS EWLTK NARQ SGKVRKNQSD TLLAVGNPAD LAVEAIRGLR TSLHFAMMEA KNNVLMISGA SPSAGMTFIS SNLAATIAIT GKKVLF IDA DLRKGYAHKM FGHKNDKGLS EFLSGQAAAE MIIDKVEGGG FDYIGRGQIP PNPAELLMHP RFEQLLNWAS QNYDLII ID TPPILAVTDA AIIGRYAGTC LLVARFEKNT VKEIDVSMKR FEQSGVVVKG CILNGVVKKA SSYYRYGHNH EGESEEDK K HHHHHH UniProtKB: UNIPROTKB: A0A778WL64 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71319 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |