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- EMDB-32004: Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-32004
TitleCryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom
Map data
Sample
  • Virus: Escherichia virus Lambda
    • Protein or peptide: Major capsid protein
Keywordsbacteriophage lambda / capsid / procapsid / capsid maturation / virus structure / cryo-EM / auxiliary protein / conformational expansion / cementing protein / DNA packaging / VIRUS
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm / Major capsid protein
Function and homology information
Biological speciesEscherichia phage lambda (virus) / Escherichia virus Lambda
Methodsingle particle reconstruction / cryo EM / Resolution: 5.03 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 26, 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: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vi9
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vi9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32004.png

Downloads & links

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Map

FileDownload / File: emd_32004.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 720 pix.
= 940.709 Å		1.31 Å/pix.
x 720 pix.
= 940.709 Å		1.31 Å/pix.
x 720 pix.
= 940.709 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025 / Movie #1: 0.0025
Minimum - Maximum-0.0121959 - 0.03528989
Average (Standard dev.)0.00022379833 (±0.0017784444)
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-0.0120.0350.000

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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

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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: VIRION / 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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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: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174346
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7vi9:
Cryo-EM structure of bacteriophage lambda procapsid at 5.03 Angstrom

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