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- EMDB-66201: LamB binding with bacteriophage Lom -

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Basic information

Entry
Database: EMDB / ID: EMD-66201
TitleLamB binding with bacteriophage Lom
Map data
Sample
  • Complex: outer membrane complex of LamB and Los
    • Protein or peptide: Maltoporin
    • Protein or peptide: Outer membrane protein lom
Keywordsmembrane protein / phage protein / complex / VIRAL PROTEIN
Function / homology
Function and homology information


maltodextrin transmembrane transporter activity / host outer membrane / maltose transporting porin activity / pore complex / monoatomic ion transport / cell outer membrane / host cell plasma membrane
Similarity search - Function
Enterobacterial Ail/Lom protein / Maltoporin / : / Enterobacterial virulence outer membrane protein signature 1. / Porin, LamB-type / Porin, LamB-type superfamily / : / LamB porin / Virulence-related outer membrane protein / Enterobacterial virulence outer membrane protein signature 2. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane protein lom / Maltoporin
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus) / Shigella sonnei (strain Ss046) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsGe XF / Wang JW
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32501078 China
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Cell Rep / Year: 2026
Title: A receptor-centered approach identifies Lom as a LamB-bound superinfection exclusion factor in bacteriophage λ.
Authors: Xiaofei Ge / Zhiwei Gu / Jiawei Wang /
Abstract: Bacteriophages face intense competition within bacterial populations. Although bacteria encode diverse anti-phage mechanisms, strategies protecting virions at the host surface remain poorly ...Bacteriophages face intense competition within bacterial populations. Although bacteria encode diverse anti-phage mechanisms, strategies protecting virions at the host surface remain poorly understood. Here, we develop a receptor-centered discovery approach that captures phage proteins bound to host receptors during infection. Applying this strategy to bacteriophage λ and its outer-membrane receptor LamB, we identify Lom as a phage-encoded outer membrane protein that binds LamB. Structural, biochemical, and functional analyses show that Lom occupies the same LamB surface recognized by the receptor-binding protein gpJ, thereby reducing phage adsorption through receptor occlusion. Ribosome profiling indicates that lom is strongly expressed during late lytic growth and is also expressed during lysogeny, consistent with a role in receptor-level superinfection exclusion. Foldseek analyses identify structurally related Lom-like proteins in diverse temperate phages, raising the possibility that receptor occlusion is a more widespread strategy. These findings establish a framework for discovering receptor-level phage competition mechanisms.
History
DepositionSep 14, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66201.png

Downloads & links

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Map

FileDownload / File: emd_66201.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 331.52 Å		1.04 Å/pix.
x 320 pix.
= 331.52 Å		1.04 Å/pix.
x 320 pix.
= 331.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-1.43549 - 2.0639215
Average (Standard dev.)0.0004291414 (±0.04457195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66201_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66201_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : outer membrane complex of LamB and Los

EntireName: outer membrane complex of LamB and Los
Components
  • Complex: outer membrane complex of LamB and Los
    • Protein or peptide: Maltoporin
    • Protein or peptide: Outer membrane protein lom

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Supramolecule #1: outer membrane complex of LamB and Los

SupramoleculeName: outer membrane complex of LamB and Los / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Lambda (virus)

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Macromolecule #1: Maltoporin

MacromoleculeName: Maltoporin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella sonnei (strain Ss046) (bacteria)
Molecular weightTheoretical: 47.568004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVDFHGYARS GIGWTGSGGE QQCFQTTGAQ SKYRLGNECE TYAELKLGQE VWKEGDKSFY FDTNVAYSVA QQNDWEATDP AFREANVQG KNLIEWLPGS TIWAGKRFYQ RHDVHMIDFY YWDISGPGAG LENIDVGFGK LSLAATRSSE AGGSSSFASN N IYDYTNET ...String:
AVDFHGYARS GIGWTGSGGE QQCFQTTGAQ SKYRLGNECE TYAELKLGQE VWKEGDKSFY FDTNVAYSVA QQNDWEATDP AFREANVQG KNLIEWLPGS TIWAGKRFYQ RHDVHMIDFY YWDISGPGAG LENIDVGFGK LSLAATRSSE AGGSSSFASN N IYDYTNET ANDVFDVRLA QMEINPGGTL ELGVDYGRAN LRDNYRLVDG ASKDGWLFTA EHTQSVLKGF NKFVVQYATD SM TSQGKGL SQGSGVAFDN EKFAYNINNN GHMLRILDHG AISMGDNWDM MYVGMYQDIN WDNDNGTKWW TVGIRPMYKW TPI MSTVME IGYDNVESQR TGDKNNQYKI TLAQQWQAGD SIWSRPAIRV FATYAKWDEK WGYDYNGDSK VNPNYGKAVP ADFN GGSFG RGDSDEWTFG AQMEIWW

UniProtKB: Maltoporin

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Macromolecule #2: Outer membrane protein lom

MacromoleculeName: Outer membrane protein lom / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 21.879734 KDa
Recombinant expressionOrganism: Escherichia phage Lambda (virus)
SequenceString: MRNVCIAVAV FAALAVTVTP ARAEGGHGTF TVGYFQVKPG TLPSLSGGDT GVSHLKGINV KYRYELTDSV GVMASLGFAA SKKSSTVMT GEDTFHYESL RGRYVSVMAG PVLQISKQVS AYAMAGVAHS RWSGSTMDYR KTEITPGYMK ETTTARDESA M RHTSVAWS ...String:
MRNVCIAVAV FAALAVTVTP ARAEGGHGTF TVGYFQVKPG TLPSLSGGDT GVSHLKGINV KYRYELTDSV GVMASLGFAA SKKSSTVMT GEDTFHYESL RGRYVSVMAG PVLQISKQVS AYAMAGVAHS RWSGSTMDYR KTEITPGYMK ETTTARDESA M RHTSVAWS AGIQINPAAS VVVDIAYEGS GSGDWRTDGF IVGVGYKF

UniProtKB: Outer membrane protein lom

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 144910
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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