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- EMDB-53608: CPS secretion pathway Wza-Wzc (Conf 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-53608
TitleCPS secretion pathway Wza-Wzc (Conf 3)
Map data
Sample
  • Complex: Wza-WzcK540M complex
    • Protein or peptide: Putative polysaccharide export protein Wza
    • Protein or peptide: Tyrosine-protein kinase wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCPS transporter / TRANSPORT PROTEIN
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 K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsYuan B / Heinz DW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: CPS secretion pathway Wza-Wzc_C8 (Conf 2)
Authors: Yuan B / Heinz DW
History
DepositionMay 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53608.png

Downloads & links

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Map

FileDownload / File: emd_53608.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 600 pix.
= 546. Å		0.91 Å/pix.
x 600 pix.
= 546. Å		0.91 Å/pix.
x 600 pix.
= 546. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05387769 - 0.20806096
Average (Standard dev.)0.0004286763 (±0.008998256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 546.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53608_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wza-WzcK540M complex

EntireName: Wza-WzcK540M complex
Components
  • Complex: Wza-WzcK540M complex
    • Protein or peptide: Putative polysaccharide export protein Wza
    • Protein or peptide: Tyrosine-protein kinase wzc
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Wza-WzcK540M complex

SupramoleculeName: Wza-WzcK540M complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Putative polysaccharide export protein Wza

MacromoleculeName: Putative polysaccharide export protein Wza / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.873832 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MMKSKMKLMP LLVSVTLISG CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGP GDVLNVTVWD HPELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP Q VDVNIAAF ...String:
MMKSKMKLMP LLVSVTLISG CTVLPGSNMS TMGKDVIKQQ DADFDLDKMV NVYPLTPRLI DQLRPRPNVA RPNMTLESEI ANYQYRVGP GDVLNVTVWD HPELTTPAGQ YRSSSDTGNW VQPDGTMFYP YIGKVHVVGK TLAEIRSDIT GRLATYIADP Q VDVNIAAF RSQKAYISGQ VNKSGQQAIT NVPLTILDAI NAAGGLTDTA DWRNVVLTHN GREERISLQA LMQNGDLNQN RL LYPGDIL YVPRNDDLKV FVMGEVKKQS TLKMDFSGMT LTEALGNAEG IDMTTSNASG IFVIRPLKGE GGRNGKIANI YQL DMSDAT SLVMATEFRL QPYDVVYVTT APVSRWNRLI NQLLPTISGV RYMTDTASDI HNWENLYFQS WSHPQFEK

UniProtKB: Putative polysaccharide export protein Wza

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Macromolecule #2: Tyrosine-protein kinase wzc

MacromoleculeName: Tyrosine-protein kinase wzc / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 81.557086 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MTEKVKQHAA PVTGSDEIDI GRLVGTVIEA RWWVIGITTV FALCAVVYTF FATPIYSADA LVQIEQNSGN SLVQDIGSAL ANKPPASDA EIQLIRSRLV LGKTVDDLDL DIAVSKNTFP IFGAGWDRLM GRQNETVKVT TFNRPKEMAD QVFTLNVLDN K NYTLSSDG ...String:
MTEKVKQHAA PVTGSDEIDI GRLVGTVIEA RWWVIGITTV FALCAVVYTF FATPIYSADA LVQIEQNSGN SLVQDIGSAL ANKPPASDA EIQLIRSRLV LGKTVDDLDL DIAVSKNTFP IFGAGWDRLM GRQNETVKVT TFNRPKEMAD QVFTLNVLDN K NYTLSSDG GFSARGQAGQ MLKKEGVTLM VEAIHASPGS EFTVTKYSTL GMINQLQNSL TVTENGKDAG VLSLTYTGED RE QIRDILN SIARNYQEQN IERKSAEASK SLAFLAQQLP EVRSRLDVAE NKLNAFRQDK DSVDLPLEAK AVLDSMVNID AQL NELTFK EAEISKLYTK VHPAYRTLLE KRQALEDEKA KLNGRVTAMP KTQQEIVRLT RDVESGQQVY MQLLNKEQEL KITE ASTVG DVRIVDPAIT QPGVLKPKKG LIILGAIILG LMLSIVGVLL RSLFNRGIES PQVLEEHGIS VYASIPLSEW QKARD SVKT IKGIKRYKQS QLLAVGNPTD LAIEAIRSLR TSLHFAMMQA QNNVLMMTGV SPSIGMTFVC ANLAAVISQT NKRVLL IDC DMRKGYTHEL LGTNNVNGLS EILIGQGDIT TAAKPTSIAK FDLIPRGQVP PNPSELLMSE RFAELVNWAS KNYDLVL ID TPPILAVTDA AIVGRHVGTT LMVARYAVNT LKEVETSLSR FEQNGIPVKG VILNSIFRRA SAYQDYGYYE YEYKSDAK S SGENLYFQGW SHPQFEK

UniProtKB: Tyrosine-protein kinase wzc

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27501
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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