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- PDB-9wcb: Open state of A8 gpJ 713 central tail fiber with OmpC G17 from E.... -

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Open data


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Basic information

Entry
Database: PDB / ID: 9wcb
TitleOpen state of A8 gpJ 713 central tail fiber with OmpC G17 from E. coli EDL933
Components
  • A8 gpJ 713
  • Outer membrane porin C
KeywordsVIRAL PROTEIN / Phage Tail
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane porin C
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Escherichia coli O157:H7 str. EDL933 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsDeng, T.Y. / Ge, X.F. / Wang, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190 China
CitationJournal: Structure / Year: 2026
Title: Structures of λ-like phage A8 tail tip bound to OmpC provide insight into receptor recognition.
Authors: Tingyue Deng / Xiaofei Ge / Jiawei Wang /
Abstract: Bacteriophage infection begins with the specific recognition of bacterial surface receptors by tail tip proteins, a decisive event that determines host specificity and triggers genome delivery. ...Bacteriophage infection begins with the specific recognition of bacterial surface receptors by tail tip proteins, a decisive event that determines host specificity and triggers genome delivery. However, the structural principles underlying this process remain poorly understood. Here, we determined high-resolution cryo-electron microscopy (cryo-EM) structures of the engineered λ-like bacteriophage A8 gpJ713 in the unbound form and bound to the outer membrane porin OmpC. Comparisons with our previously determined structures of wild-type λ gpJ alone and bound to LamB reveal conserved receptor binding-induced conformational transitions across λ-like siphoviruses, defining a general mechanistic framework for tail-tip recognition. Guided by this framework, we restored stable binding to the previously incompatible OmpC G40 variant and converted OmpF into a functional receptor through a minimal loop deletion. These proof-of-concept receptor reprogramming experiments demonstrate the predictive power of our structural model and illustrate how targeted receptor engineering can complement directed evolution in developing therapeutic phages.
History
DepositionAug 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: A8 gpJ 713
A: Outer membrane porin C
F: A8 gpJ 713
B: Outer membrane porin C
Z: A8 gpJ 713
C: Outer membrane porin C


Theoretical massNumber of molelcules
Total (without water)257,3776
Polymers257,3776
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 A8 gpJ 713


Mass: 47315.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Outer membrane porin C / Outer membrane protein 1B / Outer membrane protein C / Porin OmpC


Mass: 38476.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. EDL933 (bacteria)
Gene: ompC, Z3473, ECs3104 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XE41
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: Closed state of central tail fiber of bacteriophage lambda A8
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Lambdavirus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168284 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412351
ELECTRON MICROSCOPYf_angle_d0.58616731
ELECTRON MICROSCOPYf_dihedral_angle_d4.7231710
ELECTRON MICROSCOPYf_chiral_restr0.0451779
ELECTRON MICROSCOPYf_plane_restr0.0032238

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