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- EMDB-54649: Structure of E. coli WbaP in complex with a megabody -

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Basic information

Entry
Database: EMDB / ID: EMD-54649
TitleStructure of E. coli WbaP in complex with a megabody
Map data
Sample
  • Complex: Complex of dimeric WbaP with 2 megabody molecules
    • Organelle or cellular component: WbaP
      • Protein or peptide: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
    • Organelle or cellular component: Megabody
      • Protein or peptide: Megabody
Keywordsmembrane protein / cell wall / oligosaccharides / TRANSFERASE
Biological speciesEscherichia coli (E. coli) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWeckener M / Le Bas A / Ward PN / 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 / Naismith JH
History
DepositionAug 5, 2025-
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_54649.png

Downloads & links

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Map

FileDownload / File: emd_54649.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.0016522319 - 1.814677
Average (Standard dev.)0.0013717202 (±0.025269771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54649_msk_1.map
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Additional map: #1

Fileemd_54649_additional_1.map
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Half map: #1

Fileemd_54649_half_map_1.map
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Half map: #2

Fileemd_54649_half_map_2.map
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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
    • Organelle or cellular component: WbaP
      • Protein or peptide: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
    • Organelle or cellular component: Megabody
      • Protein or peptide: Megabody

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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: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: WbaP

SupramoleculeName: WbaP / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Megabody

SupramoleculeName: Megabody / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP

MacromoleculeName: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 57.383367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATHLARNVS CSITLAVVDF ISLTLSLYLA LGVLSLTLEH FQQRVPQDQI EGWIGLHWLL GVCCVAWYGI RLRHYFYRKT FWFELKEIL RTLVIFAIIE VAIIAFAKWY FSRYVWLMTW VFAAALVPLL RMTAKYILNS LGLWMRDTWI IGNGKNAHEA Y KAINSENN ...String:
MATHLARNVS CSITLAVVDF ISLTLSLYLA LGVLSLTLEH FQQRVPQDQI EGWIGLHWLL GVCCVAWYGI RLRHYFYRKT FWFELKEIL RTLVIFAIIE VAIIAFAKWY FSRYVWLMTW VFAAALVPLL RMTAKYILNS LGLWMRDTWI IGNGKNAHEA Y KAINSENN LGLNVVGFVD VDDNNNGSKN TIDSVQVISV DKTWLTTVDK HTQFIVAVES HQSEIRNNWL REFMIRGYRY VS VIPTLRG MPLDSTDMSF IFSHEVMIFR VQQNLAKWSS RALKRAFDIV GSLSIIIVLS PVLLYISQKV KKDGGSAIYG HER VGKGGK PFKCLKFRSM VVNSKEVLER LLENDPKAKA EWDATFKLKD DPRITKIGQF LRRTSLDELP QLFNVLKGEM SLVG PRPII TAELERYNDE VDYYLLIKPG MTGLWQVSGR SDVDYDTRVY LDAWYVKNWS MWNDIAILFK TIGVVLKKDG AYLEE NLYF QGAHHHHHHH HH

UniProtKB: UDP-Gal::undecaprenolphosphate Gal-1-P transferase WbaP

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0; 150 mM NaCl; 2 mM beta-mercaptoethanol; 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 30mA 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 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: 2902566
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1025964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8g1n


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9s7s:
Structure of E. coli WbaP in complex with a megabody

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