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- EMDB-1048: Three-dimensional structure of bacteriophage T4 baseplate. -

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Basic information

Entry
Database: EMDB / ID: EMD-1048
TitleThree-dimensional structure of bacteriophage T4 baseplate.
Map datamap contains the baseplate and the proximal part of the tail tube
Sample
  • Sample: Bacteriophage T4 baseplate-tail tube assembly
  • Protein or peptide: baseplate-tail tube complex
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / metal ion binding / identical protein binding
Similarity search - Function
Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Phage tail collar domain superfamily / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 ...Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Phage tail collar domain superfamily / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Phage tail collar domain / Phage Tail Collar Domain / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold
Similarity search - Domain/homology
Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Short tail fiber protein gp12 / Pre-baseplate central spike protein Gp5 / Baseplate central spike complex protein gp27 / Baseplate wedge protein gp6 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsKostyuchenko VA / Leiman PG / Chipman PR / Kanamaru S / vanRaaij MJ / Arisaka F / Mesyanzhinov VV / Rossmann MG
CitationJournal: Nat Struct Biol / Year: 2003
Title: Three-dimensional structure of bacteriophage T4 baseplate.
Authors: Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three- ...The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.
History
DepositionMay 19, 2003-
Header (metadata) releaseMay 19, 2003-
Map releaseSep 19, 2003-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdf
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdi
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdj
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdl
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdm
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pdp
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2fl8
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3h3w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1048.gif

Downloads & links

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Map

FileDownload / File: emd_1048.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap contains the baseplate and the proximal part of the tail tube
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.98 Å/pix.
x 196 pix.
= 583.829 Å		2.98 Å/pix.
x 196 pix.
= 583.829 Å		2.98 Å/pix.
x 196 pix.
= 583.829 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.97872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.45 / Movie #1: 2
Minimum - Maximum-7.64827013 - 10.344811440000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-98-98-97
Dimensions196196196
Spacing196196196
CellA=B=C: 583.8291 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.97871938775512.97871938775512.9787193877551
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z583.829583.829583.829
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-98-98-97
NC/NR/NS196196196
D min/max/mean-7.64810.3450.000

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Supplemental data

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Sample components

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Entire : Bacteriophage T4 baseplate-tail tube assembly

EntireName: Bacteriophage T4 baseplate-tail tube assembly
Components
  • Sample: Bacteriophage T4 baseplate-tail tube assembly
  • Protein or peptide: baseplate-tail tube complex

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Supramolecule #1000: Bacteriophage T4 baseplate-tail tube assembly

SupramoleculeName: Bacteriophage T4 baseplate-tail tube assembly / type: sample / ID: 1000 / Oligomeric state: the complex has sixfold symmetry / Number unique components: 1

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Macromolecule #1: baseplate-tail tube complex

MacromoleculeName: baseplate-tail tube complex / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage T4 (virus) / Strain: T4 18-,23- / synonym: bacteriophage T4 / Organelle: baseplate and tail tube
Recombinant expressionOrganism: Escherichia coli BE

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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

Concentration5 mg/mL
BufferpH: 7 / Details: water
GridDetails: holey carbon
VitrificationCryogen name: ETHANE / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
DateJan 30, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 15 / Average electron dose: 25 e/Å2
Details: images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel
Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000
Sample stageSpecimen holder: 626 Single Tilt Cryotransfer System / Specimen holder model: GATAN LIQUID NITROGEN

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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: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
Number images used: 945

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Atomic model buiding 1

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 2

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 3

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 4

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 5

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 6

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 7

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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Atomic model buiding 8

SoftwareName: Situs 2.0, Colores
DetailsProtocol: laplacian filtered real space
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-1pdf:
Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex

PDB-1pdi:
Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

PDB-1pdj:
Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

PDB-1pdl:
Fitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdm:
Fitting of gp8 structure into the cryoEM reconstruction of the bacteriophage T4 baseplate

PDB-1pdp:
Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

PDB-2fl8:
Fitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.

PDB-3h3w:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate

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