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Yorodumi- PDB-1pdp: Fitting of gp9 structure into the bacteriophage T4 baseplate cryo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pdp | ||||||
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Title | Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction | ||||||
Components | Baseplate structural protein Gp9 | ||||||
Keywords | STRUCTURAL PROTEIN | ||||||
Function / homology | Baseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / virus tail, baseplate / viral tail assembly / viral release from host cell / Baseplate protein gp9 Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
Authors | Kostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: Nat Struct Biol / Year: 2003 Title: Three-dimensional structure of bacteriophage T4 baseplate. Authors: Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann / Abstract: The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three- ...The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection. #1: Journal: STRUCTURE FOLD.DES. / Year: 1999 Title: The structure of bacteriophage T4 gene product 9: the trigger for tail contraction Authors: Kostyuchenko, V.A. / Navruzbekov, G.A. / Kurochkina, L.P. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
History |
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Remark 999 | SEQUENCE Only coordinates for CA atoms were submitted. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY ...BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP9 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1pdp.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pdp.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pdp_validation.pdf.gz | 819 KB | Display | wwPDB validaton report |
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Full document | 1pdp_full_validation.pdf.gz | 818.6 KB | Display | |
Data in XML | 1pdp_validation.xml.gz | 58 KB | Display | |
Data in CIF | 1pdp_validation.cif.gz | 87.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/1pdp ftp://data.pdbj.org/pub/pdb/validation_reports/pd/1pdp | HTTPS FTP |
-Related structure data
Related structure data | 1048MC 1pdfC 1pdiC 1pdjC 1pdlC 1pdmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: C6 (6 fold cyclic)) |
-Components
#1: Protein | Mass: 31024.725 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P10927 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Buffer solution | Name: water / pH: 7 / Details: water | |||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: holey carbon | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Details: ethane vitrification |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm |
Specimen holder | Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF was corrected for each particle image | ||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Method: model based projection matching / Resolution: 12 Å / Num. of particles: 945 / Nominal pixel size: 3.11 Å / Actual pixel size: 2.98 Å / Magnification calibration: TMV images / Details: a modified version of the SPIDER program was used / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: correlation coefficient / Details: REFINEMENT PROTOCOL--laplacian filtered real space | ||||||||||||
Atomic model building | PDB-ID: 1QEX Accession code: 1QEX / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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