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- PDB-1pdf: Fitting of gp11 crystal structure into 3D cryo-EM reconstruction ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pdf | ||||||
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Title | Fitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex | ||||||
![]() | Baseplate structural protein Gp11 | ||||||
![]() | STRUCTURAL PROTEIN | ||||||
Function / homology | Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / virus tail, baseplate / viral tail assembly / Baseplate wedge protein gp11![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
![]() | Kostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
![]() | ![]() 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: ![]() Title: Structure of bacteriophage T4 gene product 11, the interface between the baseplate and short tail fibers Authors: Leiman, P.G. / Kostyuchenko, V.A. / Shneider, M.M. / Kurochkina, L.P. / 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:GP11 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 117.5 KB | Display | ![]() |
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PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789 KB | Display | ![]() |
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Full document | ![]() | 788.5 KB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1048MC ![]() 1pdiC ![]() 1pdjC ![]() 1pdlC ![]() 1pdmC ![]() 1pdpC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: C6 (6 fold cyclic)) |
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Components
#1: Protein | Mass: 23725.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
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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 | |||||||||||||||
Crystal grow | *PLUS Method: electron microscopy |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001 |
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Electron gun | Electron source: ![]() |
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 |
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Processing
EM software |
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CTF correction | Details: CTF correction of each particle using Wiener filtering | ||||||||||||
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 program SPIDER was used for the reconstruction Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient maximum / Details: REFINEMENT PROTOCOL--Laplacian-filtered real space | ||||||||||||
Atomic model building | PDB-ID: 1EL6 Accession code: 1EL6 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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