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- PDB-7via: Focused refinement of asymmetric unit of bacteriophage lambda pro... -

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Basic information

Entry
Database: PDB / ID: 7via
TitleFocused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 Angstrom
ComponentsMajor capsid protein
KeywordsVIRUS / bacteriophage lambda / capsid / procapsid / capsid maturation / virus structure / cryo-EM / auxiliary protein / conformational expansion / cementing protein / DNA packaging
Function / homology
Function and homology information


T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm
Similarity search - Function
capsid protein of prophage fold / capsid protein of prophage domain / Major capsid protein GpE / Phage major capsid protein E / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsWang, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
CitationJournal: Structure / Year: 2022
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
DepositionSep 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.0Dec 15, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
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Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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Structure visualization

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)267,6047
Polymers267,6047
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26390 Å2
ΔGint-113 kcal/mol
Surface area107320 Å2

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Components

#1: Protein
Major capsid protein / Gene product E / gpE / Major head protein


Mass: 38229.160 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: E, lambdap08 / Production host: Escherichia coli (E. coli) / References: UniProt: P03713
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia virus Lambda / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia virus Lambda
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1310146 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318809
ELECTRON MICROSCOPYf_angle_d0.69725459
ELECTRON MICROSCOPYf_dihedral_angle_d4.992583
ELECTRON MICROSCOPYf_chiral_restr0.0452779
ELECTRON MICROSCOPYf_plane_restr0.0053367

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