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- PDB-3h3y: Fitting of the gp6 crystal structure into 3D cryo-EM reconstructi... -

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Database: PDB / ID: 3h3y
TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate
DescriptorBaseplate structural protein Gp6
KeywordsVIRAL PROTEIN / viral structural protein / Virion
Specimen sourcebacteriophage T4 / virus
MethodElectron microscopy (16 Å resolution / Particle / Single particle)
AuthorsAksyuk, A.A. / Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationStructure, 2009, 17, 800-808

Structure, 2009, 17, 800-808 Yorodumi Papers
The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
Anastasia A Aksyuk / Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 17, 2009 / Release: May 19, 2009
RevisionDateData content typeGroupProviderType
1.0May 19, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Deposited unit
A: Baseplate structural protein Gp6
B: Baseplate structural protein Gp6
C: Baseplate structural protein Gp6
D: Baseplate structural protein Gp6
E: Baseplate structural protein Gp6
F: Baseplate structural protein Gp6
G: Baseplate structural protein Gp6
H: Baseplate structural protein Gp6
I: Baseplate structural protein Gp6
J: Baseplate structural protein Gp6
K: Baseplate structural protein Gp6
L: Baseplate structural protein Gp6

Theoretical massNumber of molelcules
Total (without water)459,65312

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Polypeptide(L)
Baseplate structural protein Gp6 / Baseplate wedge protein 6

Mass: 38304.449 Da / Num. of mol.: 12 / Fragment: gene product 6 fragment / Mutation: residues 334 to 660 / Source: (gene. exp.) bacteriophage T4 / virus / References: UniProt: P19060

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

IDNameTypeParent ID
1T4 phages treated with 3 M ureaVIRUS0
2A ring of six gp6 dimers in the star-shaped baseplate of bacteriophage T41
Molecular weightValue: 220 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionDetails: H2O / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Temp: 100 K

Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 6, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 3400 nm / Nominal defocus min: 500 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Temperature: 100 kelvins / Tilt angle max: -9999 deg. / Tilt angle min: -9999 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: FEI
Image scansSampling size: 3.93285 microns / Number digital images: 100 / Quant bit size: 8 / Scanner model: ZEISS SCAI
Radiation wavelengthRelative weight: 1


EM software
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C6
3D reconstructionMethod: back-projection / Resolution: 16 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 1965 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3H2T
Number of atoms included #LASTProtein: 31380 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 31380

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