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- EMDB-2993: Structural rearrangements in the phage head-to-tail interface dur... -

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Basic information

Entry
Database: EMDB / ID: EMD-2993
TitleStructural rearrangements in the phage head-to-tail interface during assembly and infection
Map dataStructure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein.
Sample
  • Sample: Bacteriophage SPP1 head-to-tail interface
  • Protein or peptide: Bacteriophage SPP1 portal protein gp6
  • Protein or peptide: head completion protein gp15
  • Protein or peptide: head completion protein gp16
  • Protein or peptide: tail-to-head joining protein gp17
  • Protein or peptide: major tail protein gp17.1
Keywordsviral infection / tailed bacteriophage / Siphoviridae / SPP1 / viral assembly / head-to-tail interface / DNA gatekeeper / allosteric mechanism / concerted reorganisation / diaphragm gating
Function / homology
Function and homology information


viral head-tail joining / virus tail fiber assembly / viral DNA genome packaging, headful / virus tail, tube / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail / virion component / viral translational frameshifting
Similarity search - Function
Portal protein, SPP1-type / Portal protein, SPP1-type / : / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / : / Phage gp6-like head-tail connector protein / Portal protein / Phage portal protein, SPP1 Gp6-like / Tail completion protein ...Portal protein, SPP1-type / Portal protein, SPP1-type / : / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / : / Phage gp6-like head-tail connector protein / Portal protein / Phage portal protein, SPP1 Gp6-like / Tail completion protein / Tail completion protein / Protein of unknown function (DUF3168) / : / Bacteriophage SPP1, head-tail adaptor / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Phage major tail protein TP901-1 / Phage major tail protein TP901-1 / Phage tail tube protein / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Head completion protein gp16 / Tail completion protein gp17 / Tail tube protein gp17.1* / Portal protein / Head completion protein gp15
Similarity search - Component
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsChaban Y / Lurz R / Brasiles S / Cornilleau C / Karreman M / Zinn-Justin S / Tavares P / Orlova EV
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural rearrangements in the phage head-to-tail interface during assembly and infection.
Authors: Yuriy Chaban / Rudi Lurz / Sandrine Brasilès / Charlène Cornilleau / Matthia Karreman / Sophie Zinn-Justin / Paulo Tavares / Elena V Orlova /
Abstract: Many icosahedral viruses use a specialized portal vertex to control genome encapsidation and release from the viral capsid. In tailed bacteriophages, the portal system is connected to a tail ...Many icosahedral viruses use a specialized portal vertex to control genome encapsidation and release from the viral capsid. In tailed bacteriophages, the portal system is connected to a tail structure that provides the pipeline for genome delivery to the host cell. We report the first, to our knowledge, subnanometer structures of the complete portal-phage tail interface that mimic the states before and after DNA release during phage infection. They uncover structural rearrangements associated with intimate protein-DNA interactions. The portal protein gp6 of bacteriophage SPP1 undergoes a concerted reorganization of the structural elements of its central channel during interaction with DNA. A network of protein-protein interactions primes consecutive binding of proteins gp15 and gp16 to extend and close the channel. This critical step that prevents genome leakage from the capsid is achieved by a previously unidentified allosteric mechanism: gp16 binding to two different regions of gp15 drives correct positioning and folding of an inner gp16 loop to interact with equivalent loops of the other gp16 subunits. Together, these loops build a plug that closes the channel. Gp16 then fastens the tail to yield the infectious virion. The gatekeeper system opens for viral genome exit at the beginning of infection but recloses afterward, suggesting a molecular diaphragm-like mechanism to control DNA efflux. The mechanisms described here, controlling the essential steps of phage genome movements during virus assembly and infection, are likely to be conserved among long-tailed phages, the largest group of viruses in the Biosphere.
History
DepositionMay 3, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseJun 3, 2015-
UpdateJun 17, 2015-
Current statusJun 17, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a20
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a20
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Spp1_EMD2993...

Downloads & links

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Map

FileDownload / File: emd_2993.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 240 pix.
= 276. Å		1.15 Å/pix.
x 240 pix.
= 276. Å		1.15 Å/pix.
x 240 pix.
= 276. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.31219065 - 0.43653822
Average (Standard dev.)0.00406044 (±0.02318234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z276.000276.000276.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-0.3120.4370.004

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Supplemental data

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Sample components

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Entire : Bacteriophage SPP1 head-to-tail interface

EntireName: Bacteriophage SPP1 head-to-tail interface
Components
  • Sample: Bacteriophage SPP1 head-to-tail interface
  • Protein or peptide: Bacteriophage SPP1 portal protein gp6
  • Protein or peptide: head completion protein gp15
  • Protein or peptide: head completion protein gp16
  • Protein or peptide: tail-to-head joining protein gp17
  • Protein or peptide: major tail protein gp17.1

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Supramolecule #1000: Bacteriophage SPP1 head-to-tail interface

SupramoleculeName: Bacteriophage SPP1 head-to-tail interface / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: cyclical dodecamers and hexamers / Number unique components: 5
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Bacteriophage SPP1 portal protein gp6

MacromoleculeName: Bacteriophage SPP1 portal protein gp6 / type: protein_or_peptide / ID: 1 / Name.synonym: gp6 / Number of copies: 12 / Oligomeric state: cyclical dodecamer / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: Bacillus phage SPP1 / synonym: bacteriophage SPP1
Molecular weightExperimental: 57.2 KDa / Theoretical: 57.3225 KDa
SequenceUniProtKB: Portal protein / InterPro: Portal protein, SPP1-type

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Macromolecule #2: head completion protein gp15

MacromoleculeName: head completion protein gp15 / type: protein_or_peptide / ID: 2 / Name.synonym: gp15 / Number of copies: 12 / Oligomeric state: cyclical dodecamer / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: Bacillus phage SPP1 / synonym: bacteriophage SPP1
Molecular weightExperimental: 11.6 KDa / Theoretical: 11.6144 KDa
SequenceUniProtKB: Head completion protein gp15 / InterPro: Phage gp6-like head-tail connector protein

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Macromolecule #3: head completion protein gp16

MacromoleculeName: head completion protein gp16 / type: protein_or_peptide / ID: 3 / Name.synonym: gp16 / Number of copies: 12 / Oligomeric state: cyclical dodecamer / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: Bacillus phage SPP1 / synonym: bacteriophage SPP1
Molecular weightExperimental: 12.5 KDa / Theoretical: 12.542 KDa
SequenceUniProtKB: Head completion protein gp16 / InterPro: Bacteriophage SPP1, head-tail adaptor

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Macromolecule #4: tail-to-head joining protein gp17

MacromoleculeName: tail-to-head joining protein gp17 / type: protein_or_peptide / ID: 4 / Name.synonym: gp17 / Number of copies: 6 / Oligomeric state: cyclical hexamer / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: Bacillus phage SPP1 / synonym: bacteriophage SPP1
Molecular weightExperimental: 15 KDa / Theoretical: 15.01 KDa
SequenceUniProtKB: Tail completion protein gp17 / InterPro: Tail completion protein

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Macromolecule #5: major tail protein gp17.1

MacromoleculeName: major tail protein gp17.1 / type: protein_or_peptide / ID: 5 / Name.synonym: gp17.1 / Number of copies: 6 / Oligomeric state: cyclical hexamer / Recombinant expression: No
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: Bacillus phage SPP1 / synonym: bacteriophage SPP1
Molecular weightExperimental: 19.2 KDa / Theoretical: 19.1158 KDa
SequenceUniProtKB: Tail tube protein gp17.1* / InterPro: Phage major tail protein TP901-1

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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: 7.5 / Details: 50 mM NaCl, 50 mM Tris-Cl, 5 mM MgCl2
GridDetails: holey carbon coated Quantifoil grids (r2/2) (Quantifoil, Germany)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II / Method: blot for 2 seconds

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Electron microscopy

MicroscopeFEI POLARA 300
DateOct 9, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4 µm / Number real images: 200 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: OTHER / Software - Name: Imagic, Spider, EMAN / Number images used: 14000
Final two d classificationNumber classes: 3500

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Atomic model buiding 1

Initial modelPDB ID:

2jes

SoftwareName: Chimera, VEDA (UROX), Modeller Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5a20:
Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein

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Atomic model buiding 2

Initial modelPDB ID:

2kbz

SoftwareName: Chimera, VEDA (UROX), Modeller Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5a20:
Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein

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Atomic model buiding 3

Initial modelPDB ID:

2kca

SoftwareName: Chimera, VEDA (UROX), Modeller Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5a20:
Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein

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Atomic model buiding 4

Initial modelPDB ID:

2lfp

SoftwareName: Chimera, VEDA (UROX), Modeller Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5a20:
Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein

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