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- EMDB-8661: Cryo-EM reconstruction of the bacteriophage T4 isometric capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-8661
TitleCryo-EM reconstruction of the bacteriophage T4 isometric capsid
Map dataCryo-EM reconstruction of the bacteriophage T4 isometric capsid
Sample
  • Virus: Enterobacteria phage T4 (virus)
    • Protein or peptide: Capsid vertex protein gp24
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small outer capsid protein
    • Protein or peptide: Highly immunogenic outer capsid protein
    • Protein or peptide: Highly immunogenic outer capsid protein
KeywordsBacteriophage T4 / isometric head / virus capsid assembly / triangulation numbers / size-determining mutations / capsid stabilization / capsid decoration proteins / VIRUS
Function / homology
Function and homology information


viral capsid, decoration / T=13 icosahedral viral capsid / viral capsid
Similarity search - Function
Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain ...Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Highly immunogenic outer capsid protein / Small outer capsid protein / Major capsid protein / Highly immunogenic outer capsid protein / Capsid vertex protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen Z / Sun L
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
National Institutes of Health/Office of the DirectorS10 OD012372 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM098412-S1 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses.
Authors: Zhenguo Chen / Lei Sun / Zhihong Zhang / Andrei Fokine / Victor Padilla-Sanchez / Dorit Hanein / Wen Jiang / Michael G Rossmann / Venigalla B Rao /
Abstract: The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T = 13 ...The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) T = 13 for end caps and T = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers. The angle between adjacent hexameric capsomers is greatest around the fivefold vertices, where there is the largest deviation from a planar hexagonal array. Thus, the Soc molecules reinforce the structure where there is the greatest strain in the gp23 hexagonal lattice. Mutations that change the angles between adjacent capsomers affect the positions of the pentameric vertices, resulting in different triangulation numbers in bacteriophage T4. The analysis of the T4 mutant head assembly gives guidance to how other icosahedral viruses reproducibly assemble into capsids with a predetermined T number, although the influence of scaffolding proteins is also important.
History
DepositionApr 6, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseSep 13, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vf3
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5vf3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8661.png

Downloads & links

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Map

FileDownload / File: emd_8661.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the bacteriophage T4 isometric capsid
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy EMDB: 8.0 / Movie #1: 4
Minimum - Maximum-31.032540000000001 - 42.346490000000003
Average (Standard dev.)0.005835759 (±1.7083335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-768-768-768
Dimensions153615361536
Spacing153615361536
CellA=B=C: 1244.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z153615361536
origin x/y/z0.0000.0000.000
length x/y/z1244.1601244.1601244.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-768-768-768
NC/NR/NS153615361536
D min/max/mean-31.03342.3460.006

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Supplemental data

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Sample components

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Entire : Enterobacteria phage T4

EntireName: Enterobacteria phage T4 (virus)
Components
  • Virus: Enterobacteria phage T4 (virus)
    • Protein or peptide: Capsid vertex protein gp24
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Small outer capsid protein
    • Protein or peptide: Highly immunogenic outer capsid protein
    • Protein or peptide: Highly immunogenic outer capsid protein

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Name: gp23*-gp24*-Soc-Hoc / Diameter: 860.0 Å / T number (triangulation number): 13

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Macromolecule #1: Capsid vertex protein gp24

MacromoleculeName: Capsid vertex protein gp24 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 45.838574 KDa
SequenceString: STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTEE SKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA RFQINKWQTA V KSRKLKTG ...String:
STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTEE SKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA RFQINKWQTA V KSRKLKTG ITVELAQDLE ANGFDAPNFL EDLLATEMAD EINKDILQSL ITVSKRYKVT GITDSGFIDL SYASAPEAGR SL YRMVCEM VSHIQKESTY TATFCVASAR AAAILAASGW LKHKPEDDKY LSQNAYGFLA NGLPLYCDTN SPLDYVIVGV VEN IGEKEI VGSIFYAPYT EGLDLDDPEH VGAFKVVVDP ESLQPSIGLL VRYALSANPY TVAKDEKEAR IIDGGDMDKM AGRS DLSVL LGVKLPKIII DE

UniProtKB: Capsid vertex protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 48.728863 KDa
SequenceString: AEIGGDHGYN ATNIAAGQTS GAVTQIGPAV MGMVRRAIPN LIAFDICGVQ PMNSPTGQVF ALRAVYGKDP VAAGAKEAFH PMYGPDAMF SGQGAAKKFP ALAASTQTTV GDIYTHFFQE TGTVYLQASV QVTIDAGATD AAKLDAEIKK QMEAGALVEI A EGMATSIA ...String:
AEIGGDHGYN ATNIAAGQTS GAVTQIGPAV MGMVRRAIPN LIAFDICGVQ PMNSPTGQVF ALRAVYGKDP VAAGAKEAFH PMYGPDAMF SGQGAAKKFP ALAASTQTTV GDIYTHFFQE TGTVYLQASV QVTIDAGATD AAKLDAEIKK QMEAGALVEI A EGMATSIA ELQEGFNGST DNPWNEMGFR IDKQVIEAKS RQLKAAYSIE LTQDLRAVHG MDADAELSGI LATEIMLEIN RE VVDWINY SAQVGKSGMT LTPGSKAGVF DFQDPIDIRG ARWAGESFKA LLFQIDKEAV EIARQTGRGE GNFIIASRNV VNV LASVDT GISYAAQGLA TGFSTDTTKS VFAGVLGGKY RVYIDQYAKQ DYFTVGYKGP NEMDAGIYYA PYVALTPLRG SDPK NFQPV MGFKTRYGIG INPFAESAAQ APASRIQSGM PSILNSLGKN AYFRRVYVKG I

UniProtKB: Major capsid protein

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Macromolecule #3: Small outer capsid protein

MacromoleculeName: Small outer capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 9.085095 KDa
SequenceString:
MASARGYVNI KTFEQKLDGN KKIEGKEVSV AFPLYSDVHK ISGAHYQTFP SEKAAYSTVY EENQRTEWIA ANEDLWKVTG

UniProtKB: Small outer capsid protein

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Macromolecule #4: Highly immunogenic outer capsid protein

MacromoleculeName: Highly immunogenic outer capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 40.416547 KDa
SequenceString: MTFTVDITPK TPTGVIDETK QFTATPSGQT GGGTITYAWS VDNVPQDGAE ATFSYVLKGP AGQKTIKVVA TNTLSEGGPE TAEATTTIT VKNKTQTTTL AVTPASPAAG VIGTPVQFTA ALASQPDGAS ATYQWYVDDS QVGGETNSTF SYTPTTSGVK R IKCVAQVT ...String:
MTFTVDITPK TPTGVIDETK QFTATPSGQT GGGTITYAWS VDNVPQDGAE ATFSYVLKGP AGQKTIKVVA TNTLSEGGPE TAEATTTIT VKNKTQTTTL AVTPASPAAG VIGTPVQFTA ALASQPDGAS ATYQWYVDDS QVGGETNSTF SYTPTTSGVK R IKCVAQVT ATDYDALSVT SNEVSLTVNK KTMNPQVTLT PPSINVQQDA SATFTANVTG APEEAQITYS WKKDSSPVEG ST NVYTVDT SSVGSQTIEV TATVTAADYN PVTVTKTGNV TVTAKVAPEP EGELPYVHPL PHRSSAYIWC GWWVMDEIQK MTE EGKDWK TDDPDSKYYL HRYTLQKMMK DYPEVDVQES RNGYIIHKTA LETGIIYTYP

UniProtKB: Highly immunogenic outer capsid protein

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Macromolecule #5: Highly immunogenic outer capsid protein

MacromoleculeName: Highly immunogenic outer capsid protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 1.294587 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
Details: 50 mM sodium phosphate, pH 7.0, 75 mM sodium chloride, 1 mM magnesium chloride
GridModel: Ted Pella / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: glow discharge for 60 seconds with 30 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Blot for 8 seconds before plunging..
DetailsHigh-purity sample, volume = 50 uL, 10^12 particles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: -3.5 µm / Calibrated defocus min: -0.8 µm / Calibrated magnification: 18000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
TemperatureMin: 90.0 K / Max: 100.0 K
Alignment procedureComa free - Residual tilt: 0.5 mrad
DetailsData collection by Leginon
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 3-22 / Number grids imaged: 1 / Number real images: 3000 / Average exposure time: 9.0 sec. / Average electron dose: 26.0 e/Å2
Details: Images were collected in super-resolution mode at 40 frames per second.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19000
Details: Approximately 1000 manually-picked particles were used for 2D classification. Templates were then generated from these 2D classes and used for automated particle picking.
Startup modelType of model: NONE
Details: EMAN was used to generate an initial model from about 1000 randomly-oriented particles.
Initial angle assignmentType: COMMON LINE
Details: Randomly assigned for the particles used for initial model
Final 3D classificationNumber classes: 200 / Avg.num./class: 15 / Software - Name: RELION
Details: Relion was used for reference-free 2D classification.
Final angle assignmentType: COMMON LINE / Software - Name: EMAN, JSPR / Details: EMAN and JSPR were used for refinement.
Final reconstructionNumber classes used: 60 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Independent refinement of even/odd map, gold standard
Number images used: 18000
DetailsThe selected images were gain-normalized.

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5vf3:
Bacteriophage T4 isometric capsid

PDB-8t1x:
T4 highly immunogenic outer capsid protein C-terminal domain bound to the vertex-proximal gp23* capsomer of the isometric head in two preferred orientations

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