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- EMDB-6037: Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-... -

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Entry
Database: EMDB / ID: 6037
TitleCapsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions
KeywordsBacteriophage T7 / Maturation / DNA packaging / Procapsid / Non-covalent topological linking / Single particle cryo-EM
SampleBacteriophage T7 mature phage capsid
SourceEnterobacteria phage T7 / virus
Map dataReconstruction of bacteriophage T7 mature capsid with icosahedral symmetry averaging
Methodsingle particle (icosahedral) reconstruction, at 3.6 Å resolution
AuthorsGuo F / Liu Z / Fang PA / Zhang Q / Wright ET / Wu W / Zhang C / Vago F / Ren Y / Jakata J / Chiu W / Serwer P / Jiang W
CitationProc. Natl. Acad. Sci. U.S.A., 2014, 111, E4606-E4614

Proc. Natl. Acad. Sci. U.S.A., 2014, 111, E4606-E4614 Yorodumi Papers
Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions.
Fei Guo / Zheng Liu / Ping-An Fang / Qinfen Zhang / Elena T Wright / Weimin Wu / Ci Zhang / Frank Vago / Yue Ren / Joanita Jakana / Wah Chiu / Philip Serwer / Wen Jiang

Validation ReportPDB-ID: 3j7x

SummaryFull reportAbout validation report
DateDeposition: Aug 12, 2014 / Header (metadata) release: Sep 24, 2014 / Map release: Oct 15, 2014 / Last update: Nov 19, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.6
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 4.6
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3j7x
  • Surface level: 4.6
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3j7x
  • Imaged by Jmol
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Map

Fileemd_6037.map.gz (map file in CCP4 format, 2000001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
800 pix
1.1 Å/pix.
= 880. Å
800 pix
1.1 Å/pix.
= 880. Å
800 pix
1.1 Å/pix.
= 880. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:4.6 (by author), 4.6 (movie #1):
Minimum - Maximum-18.8522644 - 28.69979668
Average (Standard dev.)0.12035374 (1.19772434)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions800800800
Origin-400-400-400
Limit399399399
Spacing800800800
CellA=B=C: 880 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z880.000880.000880.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-18.85228.7000.120

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Supplemental data

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Sample components

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Entire Bacteriophage T7 mature phage capsid

EntireName: Bacteriophage T7 mature phage capsid / Number of components: 1
Oligomeric State: 415 copies of gp10A form T=7 icosahedral shell
MassTheoretical: 15.1 MDa

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Component #1: virus, Enterobacteria phage T7

VirusName: Enterobacteria phage T7 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 15.1 MDa
SpeciesSpecies: Enterobacteria phage T7 / virus
Source (natural)Host Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Host category: BACTERIA(EUBACTERIA)
Shell #1Name of element: mature phage capsid / Diameter: 564 Å / T number(triangulation number): 7

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 200 mM NaCl, 10 mM Tris-HCl, 1 mM MgCl2 / pH: 7.4
Support film400 mesh copper grid with one lacy carbon layer
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 90 %
Method: Blot for 2 seconds twice with 2 mm offset before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Aug 9, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 57727 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2400 nm
Specimen HolderHolder: Liquid nitrogen-cooled / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 95 K ( 80 - 100 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 364 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / OD range: 1

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 33952
Details: Particles were selected from scanned micrograph images, first automatically by the ethan method and then by manual screening with the boxer program in EMAN. The TEM instrument contrast transfer function parameters were determined automatically using fitctf2.py and were then visually validated using the EMAN ctfit program. The datasets were then divided into two subsets (even and odd) and processed completely independently, including both initial models and refinements. For 3D reconstructions, the whole datasets were divided into even-odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset. The images were first binned 4x to obtain initial models and particle parameters assuming icosahedral symmetry. De novo initial models were built using the random model approach. Random subsets of particles were assigned random initial orientations and iteratively refined until convergence. Consistent icosahedral capsid structures (other than occasional differences in handedness) were obtained by repeating the random model process. Particles with inconsistent/unstable view parameters in the initial refinements were excluded in further image processing. The orientation and center parameters were then transferred to the un-binned images for high-resolution refinements which included Simplex method-based orientation/center optimization and grid search-based refinement of defocus, astigmatism, and magnification of the images. All image refinement and reconstructions were performed with in-house developed programs jspr.py (for overall work-flow), jalign (for 2D alignment) and j3dr (for 3D reconstruction), which use EMAN and EMAN2 library functions.
3D reconstructionAlgorithm: Projection matching / Software: jspr, EMAN, EMAN2 / CTF correction: Each particle
Details: For 3D reconstruction, whole datasets were divided into even and odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset.
Resolution: 3.6 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Output model

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