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- PDB-9xgv: Colanic acid polysaccharide related protein structures -

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Basic information

Entry
Database: PDB / ID: 9xgv
TitleColanic acid polysaccharide related protein structures
Components
  • Putative polysaccharide export protein Wza
  • Tyrosine-protein kinase wzc
KeywordsPROTEIN TRANSPORT / protein transporter complex
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
Putative polysaccharide export protein Wza / Tyrosine-protein kinase wzc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsYihua, H. / Yanlong, H.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Colanic acid polysaccharide related protein structures
Authors: Jiao, L. / Yanlong, H.
History
DepositionOct 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)973,71916
Polymers973,71916
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tyrosine-protein kinase wzc


Mass: 79489.852 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: wzc, b2060, JW2045 / Production host: Escherichia coli (E. coli)
References: UniProt: P76387, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
#2: Protein
Putative polysaccharide export protein Wza


Mass: 42225.082 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: wza, b2062, JW2047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A930
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: dual complex of colanic acid polysaccharide transport channel Wza and Wzc
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65188 / Symmetry type: POINT

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