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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


ID or keywords:

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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: To Be Published
Title: Closed state of A8 gpJ 713 central tail fiber
Authors: Deng, T.Y. / Ge, X.F. / Wang, J.W.
History
DepositionAug 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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