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- PDB-3h3w: Fitting of the gp6 crystal structure into 3D cryo-EM reconstructi... -

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Database: PDB / ID: 3h3w
TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 dome-shaped baseplate
DescriptorBaseplate structural protein Gp6
KeywordsVIRAL PROTEIN / viral structural protein / Virion
Specimen sourceEnterobacteria phage T4 / virus / Bacteriophage T4
MethodElectron microscopy (12 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_5551


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

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

Cellular component

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

IDNameTypeParent IDDetails
1bacteriophage T4 dome-shaped baseplateVIRUS0
2ring of 12 molecules of gene product 61assembly of gp6 in the dome-shaped baseplate of bacteriophage T4
Buffer solutionpH: 7
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: 626 Single Tilt Cryotransfer System
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1
ReflectionD resolution high: 12 Å


EM software
1SITUS COLORESMODEL FITTINGCOLORES from the SITUS program package was used for the fitting
SymmetryPoint symmetry: C6
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 945 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 3H2T
Least-squares processHighest resolution: 12 Å
Refine hist #LASTHighest resolution: 12 Å
Number of atoms included #LASTProtein: 31380 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 31380

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