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- EMDB-12360: Wzc-K540M MgADP C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-12360
TitleWzc-K540M MgADP C1
Map data
Sample
  • Complex: Octameric complex of Wzc-K540M in complex with Mg ADP
    • Protein or peptide: Putative transmembrane protein Wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsWzc / regulator / capsular polysaccharide synthesis and transport / Gram-negative pathogens / CARBOHYDRATE
Function / homology
Function and homology information


: / protein tyrosine kinase activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsNaismith JH / Liu JW
Funding support United Kingdom, 1 items
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 12, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nii
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12360.png

Downloads & links

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Map

FileDownload / File: emd_12360.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 376 pix.
= 311.704 Å		0.83 Å/pix.
x 376 pix.
= 311.704 Å		0.83 Å/pix.
x 376 pix.
= 311.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.8372166 - 3.6118157
Average (Standard dev.)0.0064256843 (±0.07886178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 311.704 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8290.8290.829
M x/y/z376376376
origin x/y/z0.0000.0000.000
length x/y/z311.704311.704311.704
α/β/γ90.00090.00090.000
start NX/NY/NZ383838
NX/NY/NZ225225225
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS376376376
D min/max/mean-1.8373.6120.006

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Supplemental data

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Sample components

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Entire : Octameric complex of Wzc-K540M in complex with Mg ADP

EntireName: Octameric complex of Wzc-K540M in complex with Mg ADP
Components
  • Complex: Octameric complex of Wzc-K540M in complex with Mg ADP
    • Protein or peptide: Putative transmembrane protein Wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Octameric complex of Wzc-K540M in complex with Mg ADP

SupramoleculeName: Octameric complex of Wzc-K540M in complex with Mg ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 640 KDa

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Macromolecule #1: Putative transmembrane protein Wzc

MacromoleculeName: Putative transmembrane protein Wzc / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 80.571328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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 YGYSYYDK K HHHHHH

UniProtKB: Putative transmembrane protein Wzc

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 261748
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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