3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-1pdi

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

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

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

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

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

#3: With PDB-1pdf, PDB-1pdj, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w, Made 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), Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1048
CiteFit

PDB-1pdf
Cite

PDB-1pdj
Cite

PDB-1pdl
Cite

PDB-1pdm
Cite

PDB-1pdp
Cite

PDB-1h6w
 

PDB-1ocy
 

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)

Diagram

EMDB-1107

PDB-2fl8
List of similar structure data about Omokage system
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
Typepolymer
Formula weight29856.234 Da
Number of molecules18
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
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
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
Refine hist
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