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- PDB-7vi9: Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vi9 | |||||||||
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Title | Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom | |||||||||
![]() | Major capsid protein | |||||||||
![]() | VIRUS / bacteriophage lambda / capsid / procapsid / capsid maturation / virus structure / cryo-EM / auxiliary protein / conformational expansion / cementing protein / DNA packaging | |||||||||
Function / homology | Major capsid protein GpE / Phage major capsid protein E / T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm / Major capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.03 Å | |||||||||
![]() | Wang, J.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of bacteriophage lambda capsid maturation. Authors: Chang Wang / Jianwei Zeng / Jiawei Wang / ![]() Abstract: Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins ...Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins initially assemble into a precursor capsid (procapsid) and subsequent genome packaging triggers morphological expansion of the shell. An auxiliary protein is required to stabilize the expanded capsid structure. To investigate the capsid maturation mechanism, we determined the cryo-electron microscopy structures of the bacteriophage lambda procapsid and mature capsid at 3.88 Å and 3.76 Å resolution, respectively. Besides primarily rigid body movements of common features of the major capsid protein gpE, large-scale structural rearrangements of other domains occur simultaneously. Assembly of intercapsomers within the procapsid is facilitated by layer-stacking effects at 3-fold vertices. Upon conformational expansion of the capsid shell, the missing top layer is fulfilled by cementing the gpD protein against the internal pressure of DNA packaging. Our structures illuminate the assembly mechanisms of dsDNA viruses. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 402.5 KB | Display | ![]() |
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PDB format | ![]() | 337.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 825.5 KB | Display | ![]() |
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Full document | ![]() | 891.8 KB | Display | |
Data in XML | ![]() | 83.2 KB | Display | |
Data in CIF | ![]() | 126.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32004MC ![]() 7viaC ![]() 7viiC ![]() 7vikC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 38229.160 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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
Component | Name: Escherichia virus Lambda / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174346 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Refine LS restraints |
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