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

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Basic information

Entry
Database: EMDB / ID: 1048
TitleThree-dimensional structure of bacteriophage T4 baseplate.
SampleBacteriophage T4 baseplate-tail tube assembly
SourceEnterobacteria phage T4 / virus / bacteriophage T4
Map datamap contains the baseplate and the proximal part of the tail tube
Methodsingle particle reconstruction, at 12 Å resolution
AuthorsKostyuchenko VA / Leiman PG / Chipman PR / Kanamaru S / vanRaaij MJ / Arisaka F / Mesyanzhinov VV / Rossmann MG
CitationNat. Struct. Biol., 2003, 10, 688-693

Nat. Struct. Biol., 2003, 10, 688-693 StrPapers
Three-dimensional structure of bacteriophage T4 baseplate.
Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann

Validation ReportPDB-ID: 1pdf

SummaryFull report
PDB-ID: 1pdi

SummaryFull report
PDB-ID: 1pdj

SummaryFull report
PDB-ID: 1pdl

SummaryFull report
PDB-ID: 1pdm

SummaryFull report
PDB-ID: 1pdp

SummaryFull report
PDB-ID: 2fl8

SummaryFull report
PDB-ID: 3h3w

SummaryFull report
About validation report
DateDeposition: May 19, 2003 / Header (metadata) release: May 19, 2003 / Map release: Sep 19, 2003 / Last update: Oct 24, 2012

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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
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdf
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdi
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdj
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdl
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdm
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-1pdp
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-2fl8
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3h3w
  • Imaged by Jmol
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Supplemental images

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Map

Fileemd_1048.map.gz (map file in CCP4 format, 29414 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
2.98 Å/pix.
= 583.829 Å
196 pix
2.98 Å/pix.
= 583.829 Å
196 pix
2.98 Å/pix.
= 583.829 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.97872 Å
Density
Contour Level:1.45 (by author), 2 (movie #1):
Minimum - Maximum-7.64827013 - 10.34481144
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin-98-98-97
Limit979798
Spacing196196196
CellA=B=C: 583.8291 Å
α=β=γ: 90 deg.

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 / Number of components: 1 / Oligomeric State: the complex has sixfold symmetry

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Component #1: protein, baseplate-tail tube complex

ProteinName: baseplate-tail tube complex / Recombinant expression: Yes
SourceSpecies: Enterobacteria phage T4 / virus / bacteriophage T4 / Strain: T4 18-,23-
Source (engineered)Expression System: Escherichia coli be / bacteria / image: Escherichia coli
Source (natural)Organelle: baseplate and tail tube

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / Buffer solution: water / pH: 7
Support filmholey carbon
VitrificationCryogen name: ETHANE / Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 45000 X (nominal), 47000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 5000 nm
Specimen HolderHolder: 626 Single Tilt Cryotransfer System / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8
Details: images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 945 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: model based projection matching / Software: SPIDER / CTF correction: each particle
Details: modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
Resolution: 12 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #2Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #3Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #4Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #5Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #6Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #7Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Modeling #8Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space
Output model

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