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- EMDB-32011: Asymmetric unit of cryoEM structure of bacteriophage lambda capsi... -

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Basic information

Entry
Database: EMDB / ID: EMD-32011
TitleAsymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom
Map data
Sample
  • Virus: Escherichia virus Lambda
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid decoration protein
Keywordsbacteriophage lambda / capsid / procapsid / capsid maturation / virus structure / cryo-EM / auxiliary protein / conformational expansion / cementing protein / DNA packaging / VIRUS
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) / Escherichia virus Lambda
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsWang JW
Funding support China, 2 items
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, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vik
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vik
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32011.png

Downloads & links

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Map

FileDownload / File: emd_32011.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour LevelBy AUTHOR: 0.0181 / Movie #1: 0.01
Minimum - Maximum-0.027914297 - 0.067233466
Average (Standard dev.)0.000012810682 (±0.0005967779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 940.7088 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30654027777781.30654027777781.3065402777778
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z940.709940.709940.709
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-0.0280.0670.000

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Supplemental data

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Sample components

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Entire : Escherichia virus Lambda

EntireName: Escherichia virus Lambda
Components
  • Virus: Escherichia virus Lambda
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid decoration protein

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Supramolecule #1: Escherichia virus Lambda

SupramoleculeName: Escherichia virus Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10710 / Sci species name: Escherichia virus Lambda / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 38.22916 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT ...String:
MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT EWSKRDKSTY DPTDDIEAYA LNASGVVNII VFDPKGWALF RSFKAVKEKL DTRRGSNSEL ETAVKDLGKA VS YKGMYGD VAIVVYSGQY VENGVKKNFL PDNTMVLGNT QARGLRTYGC IQDADAQREG INASARYPKN WVTTGDPARE FTM IQSAPL MLLADPDEFV SVQLA

UniProtKB: Major capsid protein

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Macromolecule #2: Capsid decoration protein

MacromoleculeName: Capsid decoration protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 11.582873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTSKETFTHY QPQGNSDPAH TATAPGGLSA KAPAMTPLML DTSSRKLVAW DGTTDGAAVG ILAVAADQTS TTLTFYKSGT FRYEDVLWP EAASDETKKR TAFAGTAISI V

UniProtKB: Capsid decoration protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 835912
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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