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- PDB-7nhr: Putative transmembrane protein Wzc K540M C1 -

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Basic information

Entry
Database: PDB / ID: 7nhr
TitlePutative transmembrane protein Wzc K540M C1
ComponentsPutative transmembrane protein WzcTransmembrane protein
KeywordsCARBOHYDRATE / Wzc / regulator / capsular polysaccharide synthesis and transport / Gram-negative pathogens
Function / homology
Function and homology information


extracellular polysaccharide biosynthetic process / protein tyrosine kinase activity / phosphorylation / ATP binding / plasma membrane
Similarity search - Function
Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative transmembrane protein Wzc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsLiu, J.W. / Yang, Y. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: 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
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Putative transmembrane protein Wzc
B: Putative transmembrane protein Wzc
C: Putative transmembrane protein Wzc
D: Putative transmembrane protein Wzc
E: Putative transmembrane protein Wzc
F: Putative transmembrane protein Wzc
G: Putative transmembrane protein Wzc
H: Putative transmembrane protein Wzc


Theoretical massNumber of molelcules
Total (without water)644,5718
Polymers644,5718
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32780 Å2
ΔGint-156 kcal/mol
Surface area217330 Å2
MethodPISA

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Components

#1: Protein
Putative transmembrane protein Wzc / Transmembrane protein


Mass: 80571.328 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wzc / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X4B9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Octameric complex of Wzc-K540M / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.64 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 53.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148431 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00637565
ELECTRON MICROSCOPYf_angle_d0.69150848
ELECTRON MICROSCOPYf_dihedral_angle_d13.13714120
ELECTRON MICROSCOPYf_chiral_restr0.0486028
ELECTRON MICROSCOPYf_plane_restr0.0046509

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