+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-22441 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The bacteriophage Phi-29 viral genome packaging motor assembly | |||||||||
![]() | Focused asymmetric reconstruction of the bacteriophage phi29 dsDNA packaging motor assembly at 4.1 A. | |||||||||
![]() | Bacillus virus phi29 viral genome packaging motor assembly != Bacillus virus phi29 Bacillus virus phi29 viral genome packaging motor assembly
| |||||||||
![]() | packaging motor / ATPase / MOTOR PROTEIN | |||||||||
Function / homology | ![]() viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | White MA / Woodson M | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Authors: Michael Woodson / Joshua Pajak / Bryon P Mahler / Wei Zhao / Wei Zhang / Gaurav Arya / Mark A White / Paul J Jardine / Marc C Morais / ![]() Abstract: Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring ...Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse biological polymer manipulation tasks. Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, our results suggest that these motors cycle between helical and planar configurations, providing a possible mechanism for directional translocation of DNA. Similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 113.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 251.7 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 714.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 713.6 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jqqMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Focused asymmetric reconstruction of the bacteriophage phi29 dsDNA packaging motor assembly at 4.1 A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Bacillus virus phi29 viral genome packaging motor assembly
Entire | Name: Bacillus virus phi29 viral genome packaging motor assembly |
---|---|
Components |
|
-Supramolecule #1: Bacillus virus phi29
Supramolecule | Name: Bacillus virus phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 10756 / Sci species name: Bacillus virus phi29 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: DNA packaging protein
Macromolecule | Name: DNA packaging protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.010406 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDKSLFYNPQ KMLSYDRILN FVIGARGIGK SYAMKVYPIN RFIKYGEQFI YVRRYKPELA KVSNYFNDVA QEFPDHELVV KGRRFYIDG KLAGWAIPLS VWQSEKSNAY PNVSTIVFDE FIREKDNSNY IPNEVSALLN LMDTVFRNRE RVRCICLSNA V SVVNPYFL ...String: MDKSLFYNPQ KMLSYDRILN FVIGARGIGK SYAMKVYPIN RFIKYGEQFI YVRRYKPELA KVSNYFNDVA QEFPDHELVV KGRRFYIDG KLAGWAIPLS VWQSEKSNAY PNVSTIVFDE FIREKDNSNY IPNEVSALLN LMDTVFRNRE RVRCICLSNA V SVVNPYFL FFNLVPDVNK RFNVYDDALI EIPDSLDFSS ERRKTRFGRL IDGTEYGEMS LDNQFIGDSQ VFIEKRSKDS KF VFSIVYN GFTLGVWVDV NQGLMYIDTA HDPSTKNVYT LTTDDLNENM MLITNYKNNY HLRKLASAFM NGYLRFDNQV IRN IAYELF RKMRIQ UniProtKB: DNA packaging protein |
-Macromolecule #2: pRNA (117-MER)
Macromolecule | Name: pRNA (117-MER) / type: rna / ID: 2 / Number of copies: 5 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.469012 KDa |
Sequence | String: GGAAUGGUAC GGUACUUCCA UUGUCAUGUG UAUGUUGGGG AUUAAACCCU GAUUGAGUUC AGCCCACAUA CUUUGUUGAU UGGUUGUCA AUCAUGGCAA AAGUGCACGC UACUUUCC |
-Macromolecule #3: DNA (60-MER)
Macromolecule | Name: DNA (60-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.491848 KDa |
Sequence | String: (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC) (DA) (DG)(DT)(DC)(DA)(DG)(DT) ...String: (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC) (DA) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA) |
-Macromolecule #4: DNA (60-MER)
Macromolecule | Name: DNA (60-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.49185 KDa |
Sequence | String: (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT) (DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC) (DT)(DG)(DA)(DC)(DT)(DG) ...String: (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT) (DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC) |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: AGS |
---|---|
Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.8 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF 2002 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 0-44 / Average electron dose: 41.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 4.2 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |