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- PDB-3nb3: The host outer membrane proteins OmpA and OmpC are packed at spec... -

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Basic information

Entry
Database: PDB / ID: 3nb3
TitleThe host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components
Components
  • Outer membrane protein A
  • Outer membrane protein C
KeywordsMEMBRANE PROTEIN / virus assembly / cementing protein / bacteriophage / Sf6 / Shigella / beta-barrel / outer membrane protein / icosahedral
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity / outer membrane-bounded periplasmic space / receptor-mediated virion attachment to host cell / symbiont entry into host cell / DNA damage response / membrane / identical protein binding / metal ion binding
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Porin domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane porin C / Outer membrane protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å
AuthorsZhao, H. / Sequeira, R.D. / Galeva, N.A. / Tang, L.
CitationJournal: Virology / Year: 2011
Title: The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.
Authors: Haiyan Zhao / Reuben D Sequeira / Nadezhda A Galeva / Liang Tang /
Abstract: Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two ...Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Atomic model / Other / Source and taxonomy
Revision 1.3Nov 9, 2016Group: Other
Revision 1.4Dec 11, 2019Group: Data collection / Structure summary / Category: em_image_scans / struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.5Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Outer membrane protein A
B: Outer membrane protein A
C: Outer membrane protein A
D: Outer membrane protein C


Theoretical massNumber of molelcules
Total (without water)150,1544
Polymers150,1544
Non-polymers00
Water0
1
A: Outer membrane protein A
B: Outer membrane protein A
C: Outer membrane protein A
D: Outer membrane protein C
x 60


Theoretical massNumber of molelcules
Total (without water)9,009,255240
Polymers9,009,255240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Outer membrane protein A
B: Outer membrane protein A
C: Outer membrane protein A
D: Outer membrane protein C
x 5


  • icosahedral pentamer
  • 751 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)750,77120
Polymers750,77120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Outer membrane protein A
B: Outer membrane protein A
C: Outer membrane protein A
D: Outer membrane protein C
x 6


  • icosahedral 23 hexamer
  • 901 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)900,92624
Polymers900,92624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
DetailsCHAIN C IS LOCATED ON AN ICOSAHEDRAL 2-FOLD AXIS AND HAS 0.50 OCCUPANCY. CHAIN D IS LOCATED ON AN ICOSAHEDRAL 3-FOLD AXIS AND HAS 0.33 OCCUPANCY.

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Components

#1: Protein Outer membrane protein A / Outer membrane protein II*


Mass: 37272.672 Da / Num. of mol.: 3 / Fragment: outer membrane protein A / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A910
#2: Protein Outer membrane protein C / Porin ompC / Outer membrane protein 1B


Mass: 38336.242 Da / Num. of mol.: 1 / Fragment: outer membrane protein C / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P06996
Sequence detailsAUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE INHERITED FROM IN THE ORIGINAL PDB ENTRY 1QJP USED FOR FITTING.

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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: bacteriophage Sf6 / Type: VIRUS / Synonym: Sf6
Molecular weightValue: 19.2 MDa / Experimental value: NO
Details of virusHost category: GRAM-NEGATIVE BACTERIA / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Shigella flexneri
Virus shellName: gp5 / Diameter: 680 nm / Triangulation number (T number): 7
Buffer solutionName: 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 / pH: 7.4 / Details: 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh holey copper grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged ...Details: Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 18, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 471 nm / Nominal defocus min: 1060 nm / Cs: 4 mm
Specimen holderTemperature: 89 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC CCD (2k x 2k)

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Processing

CTF correctionDetails: none
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: model-based projection / Resolution: 19 Å / Num. of particles: 3232 / Nominal pixel size: 4.05 Å / Actual pixel size: 3.9284 Å / Magnification calibration: none
Details: The initial model was the cryoEM map of the related phage P22.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: METHOD--manual fitting in O coupled with local optimization with UCSF Chimera REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11QJP

1qjp

11QJP1PDBexperimental model
22J1N

2j1n

12J1N2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 0 0 5945

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