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

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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 / homologyBbp17 / Bbp16
Function and homology information
Specimen sourceBordetella phage BPP-1 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 2013 / Release: Dec 25, 2013
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 25, 2013Structure modelrepositoryInitial release
1.1Jan 8, 2014Structure modelDatabase references
1.2Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • 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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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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  • EMDB-5765
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers356,47014
Non-polymers00
Water0
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
Polyers21,388,229840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers1,782,35270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers2,138,82384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
major capsid protein / Bbp17


Mass: 36455.121 Da / Num. of mol.: 7 / Source: (natural) Bordetella phage BPP-1 (bacteriophage) / References: UniProt: Q775C7
#2: Protein/peptide
cementing protein / Bbp16


Mass: 14469.233 Da / Num. of mol.: 7 / Source: (natural) Bordetella phage BPP-1 (bacteriophage) / References: UniProt: Q775C8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bordetella bacteriophage / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Virus host category: BACTERIA(EUBACTERIA) / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Bordetella
Buffer solutionName: 50 mM Tris-HCl, 250 mM NaCl / Details: 50 mM Tris-HCl, 250 mM NaCl / pH: 7.5
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
MicroscopyMicroscope model: 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 FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 57660 / 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 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 895
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 39549 / Nominal pixel size: 1.1 / Actual pixel size: 1.1 / Details: (Single particle--Applied symmetry: I) / Number of class averages: 1 / Symmetry type: POINT
Number of atoms included #LASTProtein: 24653 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 24653

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