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- EMDB-22513: Satellite phage P4 procapsid including size determination (Sid) p... -

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Basic information

Entry
Database: EMDB / ID: EMD-22513
TitleSatellite phage P4 procapsid including size determination (Sid) protein
Map dataFinal masked and sharpened map reconstructed without applying symmetry from symmetry expanded particle. Normalized to mean=0 and 1 stddev.
Sample
  • Complex: P4 procapsid
    • Protein or peptide: Major capsid protein gpN
    • Protein or peptide: Size determination protein Sid
Keywordsbacteriophage / phage / procapsid / satellite phage / size determination / capsid protein / molecular piracy / VIRUS
Function / homologyBacteriophage P2, capsid / Phage major capsid protein, P2 family / viral capsid / Glycoprotein 3 / Capsid proteins
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia phage P2 (virus) / Enterobacteria phage P4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsKizziah JL / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Viruses / Year: 2020
Title: Structure of the Capsid Size-Determining Scaffold of "Satellite" Bacteriophage P4.
Authors: James L Kizziah / Cynthia M Rodenburg / Terje Dokland /
Abstract: P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the ...P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the original example of what we have termed "molecular piracy", the process by which one MGE usurps the life cycle of another for its own propagation. The P2 helper provides most of the structural gene products for assembly of the P4 virion. However, when P4 is mobilized by P2, the resulting capsids are smaller than those normally formed by P2 alone. The P4-encoded protein responsible for this size change is called Sid, which forms an external scaffolding cage around the P4 procapsids. We have determined the high-resolution structure of P4 procapsids, allowing us to build an atomic model for Sid as well as the gpN capsid protein. Sixty copies of Sid form an intertwined dodecahedral cage around the = 4 procapsid, making contact with only one out of the four symmetrically non-equivalent copies of gpN. Our structure provides a basis for understanding the mutants in gpN that prevent small capsid formation, as well as the "super-sid" mutations that counteract the effect of the mutations, and suggests a model for capsid size redirection by Sid.
History
DepositionAug 24, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jw1
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jw1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22513.png

Downloads & links

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Map

FileDownload / File: emd_22513.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal masked and sharpened map reconstructed without applying symmetry from symmetry expanded particle. Normalized to mean=0 and 1 stddev.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 864 pix.
= 959.04 Å		1.11 Å/pix.
x 864 pix.
= 959.04 Å		1.11 Å/pix.
x 864 pix.
= 959.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-21.576601 - 39.081829999999997
Average (Standard dev.)0.00000007320061 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions864864864
Spacing864864864
CellA=B=C: 959.04004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z864864864
origin x/y/z0.0000.0000.000
length x/y/z959.040959.040959.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS864864864
D min/max/mean-21.57739.0820.000

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Supplemental data

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Mask #1

Fileemd_22513_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from auto-refinement of final map.

Fileemd_22513_half_map_1.map
AnnotationHalf map 1 from auto-refinement of final map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from auto-refinement of final map.

Fileemd_22513_half_map_2.map
AnnotationHalf map 2 from auto-refinement of final map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : P4 procapsid

EntireName: P4 procapsid
Components
  • Complex: P4 procapsid
    • Protein or peptide: Major capsid protein gpN
    • Protein or peptide: Size determination protein Sid

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Supramolecule #1: P4 procapsid

SupramoleculeName: P4 procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Major capsid protein gpN

MacromoleculeName: Major capsid protein gpN / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P2 (virus)
Molecular weightTheoretical: 40.291484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRQETRFKFN AYLSRVAELN GIDAGDVSKK FTVEPSVTQT LMNTMQESSD FLTRINIVPV SEMKGEKIGI GVTGSIASTT DTAGGTERQ PKDFSKLASN KYECDQINFD FYIRYKTLDL WARYQDFQLR IRNAIIKRQS LDFIMAGFNG VKRAETSDRS S NPMLQDVA ...String:
MRQETRFKFN AYLSRVAELN GIDAGDVSKK FTVEPSVTQT LMNTMQESSD FLTRINIVPV SEMKGEKIGI GVTGSIASTT DTAGGTERQ PKDFSKLASN KYECDQINFD FYIRYKTLDL WARYQDFQLR IRNAIIKRQS LDFIMAGFNG VKRAETSDRS S NPMLQDVA VGWLQKYRNE APARVMSKVT DEEGRTTSEV IRVGKGGDYA SLDALVMDAT NNLIEPWYQE DPDLVVIVGR QL LADKYFP IVNKEQDNSE MLAADVIISQ KRIGNLPAVR VPYFPADAML ITKLENLSIY YMDDSHRRVI EENPKLDRVE NYE SMNIDY VVEDYAAGCL VEKIKVGDFS TPAKATAEPG A

UniProtKB: Capsid proteins

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Macromolecule #2: Size determination protein Sid

MacromoleculeName: Size determination protein Sid / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage P4 (virus)
Molecular weightTheoretical: 27.296814 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDHTIPEYL QPALAQLEKA RAAHLENARL MDETVTAIER AEQEKNALAQ ADGNDADDWR TAFRAAGGVL SDELKQRHIE RVARRELVQ EYDNLAVVLN FERERLKGAC DSTATAYRKA HHHLLSLYAE HELEHALNET CEALVRAMHL SILVQENPLA N TTGHQGYV ...String:
MSDHTIPEYL QPALAQLEKA RAAHLENARL MDETVTAIER AEQEKNALAQ ADGNDADDWR TAFRAAGGVL SDELKQRHIE RVARRELVQ EYDNLAVVLN FERERLKGAC DSTATAYRKA HHHLLSLYAE HELEHALNET CEALVRAMHL SILVQENPLA N TTGHQGYV APEKAVMQQV KSSLEQKIKQ MQISLTGEPV LRLTGLSAAT LPHMDYEVAG TPAQRKVWQD KIDQQGAELK AR GLLS

UniProtKB: Glycoprotein 3

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 438018
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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