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- PDB-9r67: CPS secretion pathway Wza-Wzc_C8 (Conf 1) -

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Basic information

Entry
Database: PDB / ID: 9r67
TitleCPS secretion pathway Wza-Wzc_C8 (Conf 1)
Components
  • Putative polysaccharide export protein Wza
  • Tyrosine-protein kinase wzc
KeywordsTRANSPORT PROTEIN / CPS transporter
Function / homology
Function and homology information


colanic acid metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / polysaccharide transmembrane transporter activity / colanic acid biosynthetic process / polysaccharide transport / polysaccharide biosynthetic process / porin activity / pore complex / monoatomic ion transport / cell outer membrane ...colanic acid metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / polysaccharide transmembrane transporter activity / colanic acid biosynthetic process / polysaccharide transport / polysaccharide biosynthetic process / porin activity / pore complex / monoatomic ion transport / cell outer membrane / protein tyrosine kinase activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Outer-membrane lipoprotein Wza, C-terminal domain / Outer-membrane lipoprotein Wza C-terminal domain / Polysaccharide export protein / : / Polysaccharide biosynthesis/export protein / 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 ...Outer-membrane lipoprotein Wza, C-terminal domain / Outer-membrane lipoprotein Wza C-terminal domain / Polysaccharide export protein / : / Polysaccharide biosynthesis/export protein / 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 / : / SLBB domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Putative polysaccharide export protein Wza / Tyrosine-protein kinase wzc
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYuan, B. / Heinz, D.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: CPS secretion pathway Wza-Wzc_C8 (Conf 1)
Authors: Yuan, B. / Heinz, D.W.
History
DepositionMay 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Putative polysaccharide export protein Wza
B: Putative polysaccharide export protein Wza
C: Putative polysaccharide export protein Wza
D: Putative polysaccharide export protein Wza
E: Putative polysaccharide export protein Wza
F: Putative polysaccharide export protein Wza
G: Putative polysaccharide export protein Wza
H: Putative polysaccharide export protein Wza
I: Tyrosine-protein kinase wzc
J: Tyrosine-protein kinase wzc
K: Tyrosine-protein kinase wzc
L: Tyrosine-protein kinase wzc
M: Tyrosine-protein kinase wzc
N: Tyrosine-protein kinase wzc
O: Tyrosine-protein kinase wzc
P: Tyrosine-protein kinase wzc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,006,86524
Polymers1,003,44716
Non-polymers3,4188
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative polysaccharide export protein Wza


Mass: 43873.832 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: wza, b2062, JW2047 / Production host: Escherichia coli B (bacteria) / References: UniProt: P0A930
#2: Protein
Tyrosine-protein kinase wzc


Mass: 81557.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: wzc, b2060, JW2045 / Production host: Escherichia coli B (bacteria)
References: UniProt: P76387, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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: Wza-WzcK540M-ADP complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199355 / Symmetry type: POINT

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