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- PDB-7vii: cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom -

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Basic information

Entry
Database: PDB / ID: 7vii
TitlecryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom
Components
  • Capsid decoration protein
  • Major 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


viral capsid, decoration / viral DNA genome packaging / T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm
Similarity search - Function
Head decoration protein D superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / Major capsid protein GpE / Phage major capsid protein E
Similarity search - Domain/homology
Capsid decoration protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 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 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.details
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 27, 2022Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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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
H: Capsid decoration protein
I: Capsid decoration protein
J: Capsid decoration protein
K: Capsid decoration protein
L: Capsid decoration protein
M: Capsid decoration protein
N: Capsid decoration protein


Theoretical massNumber of molelcules
Total (without water)348,68414
Polymers348,68414
Non-polymers00
Water00
1
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
H: Capsid decoration protein
I: Capsid decoration protein
J: Capsid decoration protein
K: Capsid decoration protein
L: Capsid decoration protein
M: Capsid decoration protein
N: Capsid decoration protein
x 60


Theoretical massNumber of molelcules
Total (without water)20,921,054840
Polymers20,921,054840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area49480 Å2
ΔGint-183 kcal/mol
Surface area144660 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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
H: Capsid decoration protein
I: Capsid decoration protein
J: Capsid decoration protein
K: Capsid decoration protein
L: Capsid decoration protein
M: Capsid decoration protein
N: Capsid decoration protein
x 5


  • icosahedral pentamer
  • 1.74 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,743,42170
Polymers1,743,42170
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
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
H: Capsid decoration protein
I: Capsid decoration protein
J: Capsid decoration protein
K: Capsid decoration protein
L: Capsid decoration protein
M: Capsid decoration protein
N: Capsid decoration protein
x 6


  • icosahedral 23 hexamer
  • 2.09 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,092,10584
Polymers2,092,10584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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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
#2: Protein
Capsid decoration protein / Auxiliary protein D / Gene product D / gpD / Major capsid protein D


Mass: 11582.873 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: D, lambdap07 / Production host: Escherichia coli (E. coli) / References: UniProt: P03712

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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
CTF correctionType: NONE
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88783 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424843
ELECTRON MICROSCOPYf_angle_d0.79333705
ELECTRON MICROSCOPYf_dihedral_angle_d7.0783423
ELECTRON MICROSCOPYf_chiral_restr0.0463759
ELECTRON MICROSCOPYf_plane_restr0.0074410

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