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- EMDB-5573: Focused asymmetric reconstruction VI (map 8/8): Visualization of ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5573 | |||||||||
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Title | Focused asymmetric reconstruction VI (map 8/8): Visualization of Uncorrelated Tandem Symmetry Mismatches in the Internal Genome Packaging Apparatus of a dsDNA virus | |||||||||
![]() | Focused asymmetric reconstruction (FAR-6) of bacteriophage T710A capsid I state. Display section view z=160 for core protein gp15 and z=190 for core protein gp16. | |||||||||
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![]() | bacteriophage T7 / procapsid / DNA packaging / portal / core stack / symmetry mismatch / focused asymmetric reconstruction / combinatorial assembly isomerism | |||||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / peptidoglycan metabolic process ...symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / peptidoglycan metabolic process / symbiont entry into host / viral capsid assembly / virion component / viral capsid / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
![]() | Guo F / Liu Z / Vago F / Ren Y / Wu W / Wright E / Serwer P / Jiang W | |||||||||
![]() | ![]() Title: Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7. Authors: Fei Guo / Zheng Liu / Frank Vago / Yue Ren / Weimin Wu / Elena T Wright / Philip Serwer / Wen Jiang / ![]() Abstract: Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle ...Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle electron cryomicroscopy to study the multilayer structure of the portal vertex of the bacteriophage T7 procapsid, the recipient of T7 DNA in packaging. A focused asymmetric reconstruction method was developed and applied to selectively resolve neighboring pairs of symmetry-mismatched layers of the portal vertex. However, structural features in all layers of the multilayer portal vertex could not be resolved simultaneously. Our results imply that layers with mismatched symmetries can join together in several different relative orientations, and that orientations at different interfaces assort independently to produce structural isomers, a process that we call combinatorial assembly isomerism. This isomerism explains rotational smearing in previously reported asymmetric reconstructions of the portal vertex of T7 and other bacteriophages. Combinatorial assembly isomerism may represent a new regime of structural biology in which globally varying structures assemble from a common set of components. Our reconstructions collectively validate previously proposed symmetries, compositions, and sequential order of T7 portal vertex layers, resolving in tandem the 5-fold gene product 10 (gp10) shell, 12-fold gp8 portal ring, and an internal core stack consisting of 12-fold gp14 adaptor ring, 8-fold bowl-shaped gp15, and 4-fold gp16 tip. We also found a small tilt of the core stack relative to the icosahedral fivefold axis and propose that this tilt assists DNA spooling without tangling during packaging. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 43 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
Images | ![]() | 877.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5566C ![]() 5567C ![]() 5568C ![]() 5569C ![]() 5570C ![]() 5571C ![]() 5572C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused asymmetric reconstruction (FAR-6) of bacteriophage T710A capsid I state. Display section view z=160 for core protein gp15 and z=190 for core protein gp16. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Bacteriophage T710A capsid I
Entire | Name: Bacteriophage T710A capsid I |
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Components |
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-Supramolecule #1000: Bacteriophage T710A capsid I
Supramolecule | Name: Bacteriophage T710A capsid I / type: sample / ID: 1000 / Number unique components: 6 |
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-Macromolecule #1: gp14
Macromolecule | Name: gp14 / type: protein_or_peptide / ID: 1 / Name.synonym: Internal virion protein B / Details: core stack protein / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21 KDa |
Sequence | UniProtKB: Internal virion protein gp14 |
-Macromolecule #2: gp15
Macromolecule | Name: gp15 / type: protein_or_peptide / ID: 2 / Name.synonym: Internal virion protein C / Details: core stack protein / Number of copies: 8 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 84 KDa |
Sequence | UniProtKB: Internal virion protein gp15 |
-Macromolecule #3: gp16
Macromolecule | Name: gp16 / type: protein_or_peptide / ID: 3 / Name.synonym: Internal virion protein D / Details: core stack protein / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 144 KDa |
Sequence | UniProtKB: Peptidoglycan transglycosylase gp16 |
-Macromolecule #4: gp8
Macromolecule | Name: gp8 / type: protein_or_peptide / ID: 4 / Name.synonym: Head-to-tail joining protein / Details: connector/portal / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59 KDa |
Sequence | UniProtKB: Portal protein |
-Macromolecule #5: gp10A
Macromolecule | Name: gp10A / type: protein_or_peptide / ID: 5 / Name.synonym: Major capsid protein 10A Details: major capsid protein. The correct copy number is 415. Oligomeric state: icosahedral (T=7) / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36 KDa |
Sequence | UniProtKB: Major capsid protein |
-Macromolecule #6: gp9
Macromolecule | Name: gp9 / type: protein_or_peptide / ID: 6 / Name.synonym: Capsid assembly protein / Details: scaffolding protein / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34 KDa |
Sequence | UniProtKB: Capsid assembly scaffolding protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 / Details: 200 mM NaCl, 10 mM Tris-HCl, 1 mM MgCl2 |
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Grid | Details: Ted Pella 01824, Ultrathin Carbon Film on Holey Carbon Support Film, 400 mesh, Copper |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2 seconds before plunging |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification |
Details | Parallel beam illumination |
Date | Sep 22, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1270 / Average electron dose: 25 e/Å2 / Od range: 0.6 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 57727 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TITAN KRIOS |
Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification |
Details | Parallel beam illumination |
Date | Nov 5, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1270 / Average electron dose: 25 e/Å2 / Od range: 0.6 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 57727 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected automatically by the ethan method and then by manual screening with the EMAN boxer program. CTF parameters were determined automatically using fitctf2.py and then visually validated using EMAN ctfit program. For 3-D reconstructions, the images were first binned 4x to make initial reconstructions. After alignment parameters and reconstructions converged, the 2x binned images were used for final reconstructions with a sampling of 2.2 A/pixel. |
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CTF correction | Details: phase flipping and amplitude weighted; per particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: jspr, EMAN2, EMAN Details: This is the FAR-VI map of a serials of 8 maps (Icos, SAR, FAR-I to FAR-VI). Only the core stack protein gp15, gp16 are resolved. All other proteins (gp8, gp9, gp10, gp14) are smeared. Number images used: 12360 |