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- EMDB-50046: Wzc-K540M-3YE-N711Y MgADP C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-50046
TitleWzc-K540M-3YE-N711Y MgADP C1
Map data
Sample
  • Complex: Wzc-K540M-3YE-N711Y
    • Protein or peptide: Putative transmembrane protein Wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsWzc-K540M-3YE-N711Y / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein tyrosine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase Wzc, N-terminal domain / 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: 2.71 Å
AuthorsLiu JW / Yang Y / Naismith JH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for the phosphorylation of bacterial tyrosine kinase Wzc.
Authors: Yun Yang / Mariana Batista / Bradley R Clarke / Michelle R Agyare-Tabbi / Haigang Song / Noah M Kuehfuss / Audrey Le Bas / Carol V Robinson / Chris Whitfield / Phillip J Stansfeld / James H ...Authors: Yun Yang / Mariana Batista / Bradley R Clarke / Michelle R Agyare-Tabbi / Haigang Song / Noah M Kuehfuss / Audrey Le Bas / Carol V Robinson / Chris Whitfield / Phillip J Stansfeld / James H Naismith / Jiwei Liu /
Abstract: The regulation of polymerisation and translocation of biomolecules is fundamental. Wzc, an integral cytoplasmic membrane tyrosine autokinase protein serves as the master regulator of the biosynthesis ...The regulation of polymerisation and translocation of biomolecules is fundamental. Wzc, an integral cytoplasmic membrane tyrosine autokinase protein serves as the master regulator of the biosynthesis and export of many bacterial capsular polysaccharides and exopolysaccharides. Such polysaccharides play essential roles in infection, defence, and some are important industrial products. Wzc comprises a large periplasmic domain, two transmembrane helices and a C-terminal cytoplasmic kinase domain with a tyrosine-rich tail. Wzc regulates polymerisation functions through cycling the formation and dissociation of an octameric complex, driven by changes in the phosphorylation status of the tyrosine-rich tail. E. coli Wzc serves a model for a wider family of polysaccharide co-polymerases. Here, we determine structures of intermediate states with different extents of phosphorylation. Structural and computational data reveal the pre-ordering of the tyrosine-rich tail, the molecular basis underlying the unidirectionality of phosphorylation events, and the underlying structural dynamics on how phosphorylation status is transmitted.
History
DepositionApr 8, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50046.png

Downloads & links

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Map

FileDownload / File: emd_50046.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.)
0.74 Å/pix.
x 376 pix.
= 277.112 Å		0.74 Å/pix.
x 376 pix.
= 277.112 Å		0.74 Å/pix.
x 376 pix.
= 277.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.737 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.89806104 - 1.5348998
Average (Standard dev.)0.002872543 (±0.03365434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 277.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50046_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50046_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Wzc-K540M-3YE-N711Y

EntireName: Wzc-K540M-3YE-N711Y
Components
  • Complex: Wzc-K540M-3YE-N711Y
    • Protein or peptide: Putative transmembrane protein Wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Wzc-K540M-3YE-N711Y

SupramoleculeName: Wzc-K540M-3YE-N711Y / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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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: 80.518234 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 SSYYRYGHYH YGESEEDK 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: FEI FALCON IV (4k x 4k) / Average electron dose: 31.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
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: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 413751
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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