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- PDB-7ni2: Wzc-K540M-4YE C8 -

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Basic information

Entry
Database: PDB / ID: 7ni2
TitleWzc-K540M-4YE C8
ComponentsTyrosine-protein kinase
KeywordsCARBOHYDRATE / Wzc / regulator / capsular polysaccharide synthesis and transport / Gram-negative pathogens
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsNaismith, J.H. / Liu, J.W. / Yang, Y.
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
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Tyrosine-protein kinase
B: Tyrosine-protein kinase
C: Tyrosine-protein kinase
D: Tyrosine-protein kinase
E: Tyrosine-protein kinase
F: Tyrosine-protein kinase
G: Tyrosine-protein kinase
H: Tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)643,4818
Polymers643,4818
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22960 Å2
ΔGint-79 kcal/mol
Surface area190500 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEGLYC1 - 510
d_21ens_1ILEGLYB1 - 510
d_31ens_1ILEGLYA1 - 510
d_41ens_1ILEGLYD1 - 510
d_51ens_1ILEGLYE1 - 510
d_61ens_1ILEGLYF1 - 510
d_71ens_1ILEGLYG1 - 510
d_81ens_1ILEGLYH1 - 510

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Components

#1: Protein
Tyrosine-protein kinase


Mass: 80435.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GE031_21350 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A778WL64, non-specific protein-tyrosine kinase

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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-4YE / 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 FIELD
Image recordingElectron dose: 57.5 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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71319 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00731808
ELECTRON MICROSCOPYf_angle_d0.68743104
ELECTRON MICROSCOPYf_dihedral_angle_d13.3511872
ELECTRON MICROSCOPYf_chiral_restr0.0495208
ELECTRON MICROSCOPYf_plane_restr0.0055480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints0.000724842782595
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.000708444218827
ens_1d_4CELECTRON MICROSCOPYNCS constraints0.00071088574511
ens_1d_5CELECTRON MICROSCOPYNCS constraints0.000713416186382
ens_1d_6CELECTRON MICROSCOPYNCS constraints0.000709985343054
ens_1d_7CELECTRON MICROSCOPYNCS constraints0.000707757392882
ens_1d_8CELECTRON MICROSCOPYNCS constraints0.000882656304757

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