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- EMDB-58108: Structure of E. coli WbaP in complex with a megabody in the prese... -

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Basic information

Entry
Database: EMDB / ID: EMD-58108
TitleStructure of E. coli WbaP in complex with a megabody in the presence of UDP-Gal processed in C2 symmetry
Map dataEM map
Sample
  • Complex: Complex of dimeric WbaP with 2 megabody molecules
    • Protein or peptide: Undecaprenyl-phosphate galactose phosphotransferase WbaP
    • Protein or peptide: Megabody
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE
Keywordsmembrane protein / cell wall / oligosaccharides / transferase
Biological speciesEscherichia coli (E. coli) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWeckener M / Le Bas A / Ward PN / Harrison PJ / Naismith JH
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust220526/Z/20/Z United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Structural and functional studies of the polytopic phosphoglycosyltransferase WbaP in E. coli
Authors: Weckener M / Le Bas A / Ward PN / Harrison PJ / Naismith JH
History
DepositionMay 14, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58108.png

Downloads & links

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Map

FileDownload / File: emd_58108.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 336.896 Å		0.66 Å/pix.
x 512 pix.
= 336.896 Å		0.66 Å/pix.
x 512 pix.
= 336.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.066341735 - 0.118747585
Average (Standard dev.)0.00000083977585 (±0.0022683458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 336.896 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58108_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_58108_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_58108_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of dimeric WbaP with 2 megabody molecules

EntireName: Complex of dimeric WbaP with 2 megabody molecules
Components
  • Complex: Complex of dimeric WbaP with 2 megabody molecules
    • Protein or peptide: Undecaprenyl-phosphate galactose phosphotransferase WbaP
    • Protein or peptide: Megabody
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of dimeric WbaP with 2 megabody molecules

SupramoleculeName: Complex of dimeric WbaP with 2 megabody molecules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Undecaprenyl-phosphate galactose phosphotransferase WbaP

MacromoleculeName: Undecaprenyl-phosphate galactose phosphotransferase WbaP
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 57.450438 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTHLARNVSC SITLAVVDFI SLTLSLYLAL GVLSLTLEHF QQRVPQDQIE GWIGLHWLLG VCCVAWYGIR LRHYFYRKTF WFELKEILR TLVIFAIIEV AIIAFAKWYF SRYVWLMTWV FAAALVPLLR MTAKYILNSL GLWMRDTWII GNGKNAHEAY K AINSENNL ...String:
MTHLARNVSC SITLAVVDFI SLTLSLYLAL GVLSLTLEHF QQRVPQDQIE GWIGLHWLLG VCCVAWYGIR LRHYFYRKTF WFELKEILR TLVIFAIIEV AIIAFAKWYF SRYVWLMTWV FAAALVPLLR MTAKYILNSL GLWMRDTWII GNGKNAHEAY K AINSENNL GLNVVGFVDV DDNNNGSKNT IDSVQVISVD KTWLTTVDKH TQFIVAVESH QSEIRNNWLR EFMIRGYRYV SV IPTLRGM PLDSTDMSFI FSHEVMIFRV QQNLAKWSSR ALKRAFDIVG SLSIIIVLSP VLLYISQKVK KDGGSAIYGH ERV GKGGKP FKCLKFRSMV VNSKEVLERL LENDPKAKAE WDATFKLKDD PRITKIGQFL RRTSLDELPQ LFNVLKGEMS LVGP RPIIT AELERYNDEV DYYLLIKPGM TGLWQVSGRS DVDYDTRVYL DAWYVKNWSM WNDIAILFKT IGVVLKKDGA YLEEN LYFQ GAHHHHHHHH HH

UniProtKB: UNIPROTKB: A0A6D1CLM9

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Macromolecule #2: Megabody

MacromoleculeName: Megabody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 56.575027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLVESGGG LVLKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTAG GGKNSCATFG AEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ AEILKLANQV ESDFNKLSSG H LKDYIGKC ...String:
QVQLVESGGG LVLKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTAG GGKNSCATFG AEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ AEILKLANQV ESDFNKLSSG H LKDYIGKC DASAISSANM TMQNQKNNWG NGCAGVEETQ SLLKTSAADF NNQTPQINQA QNLANTLIQE LGNNTYEQLS RL LTNDNGT NSKTSAQAIN QAVNNLNERA KTLAGGTTNS PAYQATLLAL RSVLGLWNSM GYAVICGGYT KSPGENNQKD FHY TDENGN GTTINCGGST NSNGTHSYNG TNTLKADKNV SLSIEQYEKI HEAYQILSKA LKQAGLAPLN SKGEKLEAHV TTSK SSLRL SCTASGRTFS SYAMGWFRQP PGKEREFVAS IMGSGSNIYY ADSVKGRFTI SRDNAKNTLY LQMNSLKPED TAVYY CAAD PRPLSYSSSY YYRSGSYDYW GQGTQVTVSS HHHHHHEPEA

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Macromolecule #3: GALACTOSE-URIDINE-5'-DIPHOSPHATE

MacromoleculeName: GALACTOSE-URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GDU
Molecular weightTheoretical: 566.302 Da
Chemical component information

ChemComp-GDU:
GALACTOSE-URIDINE-5'-DIPHOSPHATE

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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

Concentration2 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM beta-merecaptoethanol, 0.001% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Grids were glow discharged twice at 30 mM for 30s each
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5021937
CTF correctionSoftware - Name: cryoSPARC (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5) / Number images used: 492904
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-30wc:
Structure of E. coli WbaP in complex with a megabody in the presence of UDP-Gal processed in C2 symmetry

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