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

by single particle reconstruction, at 12 A resolution

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#2: Superimposing with simplified surface model of EM map, EMDB-1048, Image by Jmol

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#4: Superimposing with EM 3D map: EMDB-1048 (with PDB-1pdf, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1pdi
TitleFitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
DescriptorShort tail fiber protein
KeywordsSTRUCTURAL PROTEIN
AuthorsKostyuchenko, V.A., Leiman, P.G., Chipman, P.R., Kanamaru, S., van Raaij, M.J., Arisaka, F., Mesyanzhinov, V.V., Rossmann, M.G.
DateDeposition: 2003-05-19, Release: 2003-09-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1048, Image by Jmol

#3: With PDB-1pdf, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1048 (with PDB-1pdf, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w), Image by UCSF CHIMERA

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EMDB-1048

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Article
Citation - primary
ArticleNat. Struct. Biol., Vol. 10, Issue 9, Page 688-93, Year 2003
TitleThree-dimensional structure of bacteriophage T4 baseplate.
AuthorsVictor A Kostyuchenko, Petr G Leiman, Paul R Chipman, Shuji Kanamaru, Mark J van Raaij, Fumio Arisaka, Vadim V Mesyanzhinov, Michael G Rossmann
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., 117997 Moscow, Russia.
KeywordsBacteriophage T4 (chemistry), Cryoelectron Microscopy, Image Processing, Computer-Assisted, Microscopy, Electron, Models, Molecular, Protein Structure, Tertiary
LinksPubMed: 12923574, DOI: 10.1038/nsb970
Citation - 1
ArticleJ.Mol.Biol., Vol. 314, Page: 1137 - 1146, Year: 2001,
TitleCrystal Structure of a Heat-and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
Authorsvan Raaij, M.J., Schoehn, G., Burda, M.R., Miller, S.
Citation - 2
ArticleTo be published, Vol. , Page: - , Year: ,
TitleStructure of the receptor-binding domain of the bacteriophage T4 short tail fibre
AuthorsThomassen, E., Gielen, G., Schuetz, M., Miller, S., van Raaij, M.J.
Components
ID 1 : Protein Gp12, p12
Image
DescriptionShort tail fiber protein
Typepolypeptide(L)
Formula weight29856.234 Da
Number of molecules18
ID1
SourceMethod: Isolated from a natural source
Genus: T4-like viruses
NCBI taxonomy: ID:10665
Organism scientific: Enterobacteria phage T4
Species: Enterobacteria phage T4 sensu lato
Strain: T4D
LinksUniProt: P10930, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsT4 double mutant, 18-,23-, produces baseplate-tail tube assemblies
NameT4 baseplate-tail tube complex
Entity assembly
Assembly-ID1
Detailstrimer
Namegp12
Buffer
Namewater
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7
Sample concentration5 mg/ml
Sample support
Detailsholey carbon
Vitrification
Detailsethane vitrification
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM300FEG/T
Date2001-01-30
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose25 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 47000 X, Nominal: 45000 X
CsNominal: 2 mm
Nominal defocusMax: 5000 nm, Min: 1200 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature70 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Number of particles945
Software namesitus 2.0/colores
Single particle entity
Symmetry typeCYCLIC
3D reconstruction
Actual pixel size2.98 A/pix
CTF correction methodCTF correction of individual particles with Wiener filtering
Detailsmodifed version of program SPIDER was used for the reconstruction
Magnification calibrationTMV particles images
Methodmodel-based projection matching
Nominal pixel size3.11 A/pix
Resolution12.0 A
3D fitting
Refinement ProtocolLaplacian transform real space
Refinement SpaceREAL
Software namesitus 2.0/colores
Target criteriaCorrelation Coefficient maximization
3D fitting list
3D Fitting ID1
PDB entry ID1OCY
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms5004
Protein atoms5004
Download
PDB format
Allpdb1pdi.ent.gz
pdb1pdi.ent (uncompressed file)
Header onlypdb1pdi.ent.gz
mmCIF format
mmCIF1pdi.cif.gz
XML format
All1pdi.xml.gz
No-atom1pdi-noatom.xml.gz
Ext-atom1pdi-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.5 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB