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- EMDB-3572: Localized reconstruction of bacteriophage phi6 packaging hexamer P4 -

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Basic information

Entry
Database: EMDB / ID: EMD-3572
TitleLocalized reconstruction of bacteriophage phi6 packaging hexamer P4
Map dataLocalized reconstruction of bacteriophage phi6 packaging hexamer P4 in situ
Sample
  • Virus: Pseudomonas phage phi6 (bacteriophage)
    • Protein or peptide: Packaging enzyme P4
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordspackaging / ATPase / vertex / hyrdolase / HYDROLASE
Function / homology
Function and homology information


viral procapsid / viral genome packaging / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / viral capsid / ATP binding
Similarity search - Function
Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsSun Z / El Omari K
CitationJournal: Nucleic Acids Res / Year: 2013
Title: Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.
Authors: Kamel El Omari / Christoph Meier / Denis Kainov / Geoff Sutton / Jonathan M Grimes / Minna M Poranen / Dennis H Bamford / Roman Tuma / David I Stuart / Erika J Mancini /
Abstract: Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, ...Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.
History
DepositionJan 14, 2017-
Header (metadata) releaseJan 25, 2017-
Map releaseMar 22, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5muv
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5muv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3572.png

Downloads & links

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Map

FileDownload / File: emd_3572.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstruction of bacteriophage phi6 packaging hexamer P4 in situ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 128 pix.
= 172.8 Å		1.35 Å/pix.
x 128 pix.
= 172.8 Å		1.35 Å/pix.
x 128 pix.
= 172.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.019164821 - 0.029692305
Average (Standard dev.)-0.007869697 (±0.0052563194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 172.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z172.800172.800172.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0190.030-0.008

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Supplemental data

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Sample components

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Entire : Pseudomonas phage phi6

EntireName: Pseudomonas phage phi6 (bacteriophage)
Components
  • Virus: Pseudomonas phage phi6 (bacteriophage)
    • Protein or peptide: Packaging enzyme P4
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Pseudomonas phage phi6

SupramoleculeName: Pseudomonas phage phi6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Pseudomonas syringae (bacteria)

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Macromolecule #1: Packaging enzyme P4

MacromoleculeName: Packaging enzyme P4 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: nucleoside-triphosphate phosphatase
Source (natural)Organism: Pseudomonas phage phi6 (bacteriophage)
Molecular weightTheoretical: 32.67874 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD ...String:
MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD EMLIVCIGLG ALGFNVAVDS VRPLLFRLKG AASAGGIVAV FYSLLTDISN LFTQYDCSVV MVVNPMVDAE KI EYVFGQV MASTVGAILC ADGNVSRTMF RTNKGRIFNG AAPLAADTHM PSMDRPTSMK ALDHTSIASV AP

UniProtKB: Packaging enzyme P4

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.2
GridModel: C-flat / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80.0 K / Max: 120.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-22 / Number real images: 900 / Average exposure time: 0.2 sec. / Average electron dose: 0.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 159492
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 56448
Initial angle assignmentType: OTHER / Software - Version: 1.1.0 / Software - details: LocalizedReconstruction
Details: Angles for P4 hexameter sub-particles were calculated from particle orientations
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5muv:
Atomic structure fitted into a localized reconstruction of bacteriophage phi6 packaging hexamer P4

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