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Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate

by single particle reconstruction, at 12 A resolution

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#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-1pdi, 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-1pdi, PDB-1pdl, PDB-1pdm, PDB-1pdp, PDB-2fl8, PDB-3h3w), Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1pdj
TitleFitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate
DescriptorBaseplate structural protein Gp27
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-1pdi, 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-1pdi, 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-1pdi
Cite

PDB-1pdl
Cite

PDB-1pdm
Cite

PDB-1pdp
Cite

PDB-1k28
 

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)

Diagram

EMDB-2067

PDB-4aoe
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
ArticleNature, Vol. 415, Page: 553 - 557, Year: 2002,
TitleStructure of the cell-puncturing device of bacteriophage T4
AuthorsKanamaru, S., Leiman, P.G., Kostyuchenko, V.A., Chipman, P.R., Mesyanzhinov, V.V., Arisaka, F., Rossmann, M.G.
Components
ID 1 : Hub protein 27
Image
DescriptionBaseplate structural protein Gp27
Typepolypeptide(L)
Formula weight44431.465 Da
Number of molecules3
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
LinksUniProt: P17172, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameT4 baseplate-tail tube complex
Entity assembly
Assembly-ID1
Detailstrimer
Namegp27
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 was corrected for each particle with Wiener filtering
Detailsa modified version of SPIDER was used for the reconstruction
Magnification calibrationTMV images
Methodmodel based projection matching
Nominal pixel size3.11 A/pix
Resolution12 A
3D fitting
Refinement Protocollaplacian filtered real space
Refinement SpaceREAL
Software namesitus 2.0/colores
Target criteriaCorrelation coefficient maximization
3D fitting list
3D fitting id1
PDB entry ID1K28

PDB-1k28
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1092
Protein atoms1092
Download
PDB format
Allpdb1pdj.ent.gz
pdb1pdj.ent (uncompressed file)
Header onlypdb1pdj.ent.gz
mmCIF format
mmCIF1pdj.cif.gz
XML format
All1pdj.xml.gz
No-atom1pdj-noatom.xml.gz
Ext-atom1pdj-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB