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- PDB-3j4u: A new topology of the HK97-like fold revealed in Bordetella bacte... -

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Basic information

Entry
Database: PDB / ID: 3j4u
TitleA new topology of the HK97-like fold revealed in Bordetella bacteriophage: non-covalent chainmail secured by jellyrolls
Components
  • cementing protein
  • major capsid protein
KeywordsVIRUS / protein topology / cryoEM
Function / homology
Function and homology information


Jelly Rolls - #1110 / : / Bbp16 / : / Major capsid protein GP7 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBordetella phage BPP-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, X. / Guo, H. / Jin, L. / Czornyj, E. / Hodes, A. / Hui, W.H. / Nieh, A.W. / Miller, J.F. / Zhou, Z.H.
CitationJournal: Elife / Year: 2013
Title: A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution.
Authors: Xing Zhang / Huatao Guo / Lei Jin / Elizabeth Czornyj / Asher Hodes / Wong H Hui / Angela W Nieh / Jeff F Miller / Z Hong Zhou /
Abstract: Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering ...Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like ('Johnson') for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 23 hexamer
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Assembly

Deposited unit
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
H: cementing protein
I: cementing protein
J: cementing protein
K: cementing protein
L: cementing protein
M: cementing protein
N: cementing protein


Theoretical massNumber of molelcules
Total (without water)356,47014
Polymers356,47014
Non-polymers00
Water00
1
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
H: cementing protein
I: cementing protein
J: cementing protein
K: cementing protein
L: cementing protein
M: cementing protein
N: cementing protein
x 60


Theoretical massNumber of molelcules
Total (without water)21,388,229840
Polymers21,388,229840
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: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
H: cementing protein
I: cementing protein
J: cementing protein
K: cementing protein
L: cementing protein
M: cementing protein
N: cementing protein
x 5


  • icosahedral pentamer
  • 1.78 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,782,35270
Polymers1,782,35270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
H: cementing protein
I: cementing protein
J: cementing protein
K: cementing protein
L: cementing protein
M: cementing protein
N: cementing protein
x 6


  • icosahedral 23 hexamer
  • 2.14 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,138,82384
Polymers2,138,82384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
major capsid protein / Bbp17


Mass: 36455.121 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bordetella phage BPP-1 (virus) / References: UniProt: Q775C7
#2: Protein
cementing protein / Bbp16


Mass: 14469.233 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bordetella phage BPP-1 (virus) / References: UniProt: Q775C8

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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: Bordetella bacteriophage / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Bordetella
Buffer solutionName: 50 mM Tris-HCl, 250 mM NaCl / pH: 7.5 / Details: 50 mM Tris-HCl, 250 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh holey carbon film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 12, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 57660 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Astigmatism: manual correction
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 895
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1eLite3D3D reconstruction
2FREALIGN3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39549 / Nominal pixel size: 1.1 Å / Actual pixel size: 1.1 Å / Details: (Single particle--Applied symmetry: I) / Num. of class averages: 1 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms24653 0 0 0 24653

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