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- EMDB-4706: Bacteriophage ejection complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4706
TitleBacteriophage ejection complex
Map dataBacteriophage ejection complex
Sample
  • Complex: Bacteriophage tail complex
    • Complex: Portal protein
      • Protein or peptide: Portal protein
    • Complex: Adaptor protein
      • Protein or peptide: Tail tubular protein gp11
    • Complex: Nozzle protein
      • Protein or peptide: Tail tubular protein gp12
Keywordsviral complex / DNA ejection / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging
Similarity search - Function
Tail tubular protein Gp11 / Tail tubular protein / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein
Similarity search - Domain/homology
Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsCuervo A / Fabrega-Ferrer M
Funding support Spain, 7 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-09071 Spain
European Commission653706
CitationJournal: Nat Commun / Year: 2019
Title: Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism.
Authors: Ana Cuervo / Montserrat Fàbrega-Ferrer / Cristina Machón / José Javier Conesa / Francisco J Fernández / Rosa Pérez-Luque / Mar Pérez-Ruiz / Joan Pous / M Cristina Vega / José L Carrascosa / Miquel Coll /
Abstract: Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been ...Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
History
DepositionMar 15, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseSep 4, 2019-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0113
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0113
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r21
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4706.png

Downloads & links

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Map

FileDownload / File: emd_4706.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage ejection complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 350 pix.
= 366.8 Å		1.05 Å/pix.
x 350 pix.
= 366.8 Å		1.05 Å/pix.
x 350 pix.
= 366.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0113 / Movie #1: 0.0113
Minimum - Maximum-0.002652 - 0.255892
Average (Standard dev.)0.00077379897 (±0.006800785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 366.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z366.800366.800366.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-39-149-104
NX/NY/NZ201201211
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0030.2560.001

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Supplemental data

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Sample components

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Entire : Bacteriophage tail complex

EntireName: Bacteriophage tail complex
Components
  • Complex: Bacteriophage tail complex
    • Complex: Portal protein
      • Protein or peptide: Portal protein
    • Complex: Adaptor protein
      • Protein or peptide: Tail tubular protein gp11
    • Complex: Nozzle protein
      • Protein or peptide: Tail tubular protein gp12

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Supramolecule #1: Bacteriophage tail complex

SupramoleculeName: Bacteriophage tail complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterobacteria phage T7 (virus)
Molecular weightTheoretical: 534 KDa

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Supramolecule #2: Portal protein

SupramoleculeName: Portal protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Enterobacteria phage T7 (virus)

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Supramolecule #3: Adaptor protein

SupramoleculeName: Adaptor protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Enterobacteria phage T7 (virus)

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Supramolecule #4: Nozzle protein

SupramoleculeName: Nozzle protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Enterobacteria phage T7 (virus)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T7 (virus)
Molecular weightTheoretical: 59.173984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV ...String:
MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV QRDAFGNVLQ MVTRDQIAFG ALPEDIRKAV EGQGGEKKAD ETIDVYTHIY LDEDSGEYLR YEEVEGMEVQ GS DGTYPKE ACPYIPIRMV RLDGESYGRS YIEEYLGDLR SLENLQEAIV KMSMISSKVI GLVNPAGITQ PRRLTKAQTG DFV TGRPED ISFLQLEKQA DFTVAKAVSD AIEARLSFAF MLNSAVQRTG ERVTAEEIRY VASELEDTLG GVYSILSQEL QLPL VRVLL KQLQATQQIP ELPKEAVEPT ISTGLEAIGR GQDLDKLERC VTAWAALAPM RDDPDINLAM IKLRIANAIG IDTSG ILLT EEQKQQKMAQ QSMQMGMDNG AAALAQGMAA QATASPEAMA AAADSVGLQP GI

UniProtKB: Portal protein

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Macromolecule #2: Tail tubular protein gp11

MacromoleculeName: Tail tubular protein gp11 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T7 (virus)
Molecular weightTheoretical: 26.20282 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GMASMTGGNN MGRDLYDDDD KDPSSMRSYD MNVETAAELS AVNDILASIG EPPVSTLEGD ANADAANARR ILNKINRQI QSRGWTFNIE EGITLLPDVY SNLIVYSDDY LSLMSTSGQS IYVNRGGYVY DRTSQSDRFD SGITVNIIRL R DYDEMPEC ...String:
MRGSHHHHHH GMASMTGGNN MGRDLYDDDD KDPSSMRSYD MNVETAAELS AVNDILASIG EPPVSTLEGD ANADAANARR ILNKINRQI QSRGWTFNIE EGITLLPDVY SNLIVYSDDY LSLMSTSGQS IYVNRGGYVY DRTSQSDRFD SGITVNIIRL R DYDEMPEC FRYWIVTKAS RQFNNRFFGA PEVEGVLQEE EDEARRLCME YEMDYGGYNM LDGDAFTSGL LTR

UniProtKB: Tail tubular protein gp11

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Macromolecule #3: Tail tubular protein gp12

MacromoleculeName: Tail tubular protein gp12 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T7 (virus)
Molecular weightTheoretical: 89.480594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH ...String:
MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH INGKDVAKYK IPDGSQPEHV NNTDAQWLAE ELAKQMRTNL SDWTVNVGQG FIHVTAPSGQ QIDSFTTKDG YA DQLINPV THYAQSFSKL PPNAPNGYMV KIVGDASKSA DQYYVRYDAE RKVWTETLGW NTEDQVLWET MPHALVRAAD GNF DFKWLE WSPKSCGDVD TNPWPSFVGS SINDVFFFRN RLGFLSGENI ILSRTAKYFN FYPASIANLS DDDPIDVAVS TNRI AILKY AVPFSEELLI WSDEAQFVLT ASGTLTSKSV ELNLTTQFDV QDRARPFGIG RNVYFASPRS SFTSIHRYYA VQDVS SVKN AEDITSHVPN YIPNGVFSIC GSGTENFCSV LSHGDPSKIF MYKFLYLNEE LRQQSWSHWD FGENVQVLAC QSISSD MYV ILRNEFNTFL ARISFTKNAI DLQGEPYRAF MDMKIRYTIP SGTYNDDTFT TSIHIPTIYG ANFGRGKITV LEPDGKI TV FEQPTAGWNS DPWLRLSGNL EGRMVYIGFN INFVYEFSKF LIKQTADDGS TSTEDIGRLQ LRRAWVNYEN SGTFDIYV E NQSSNWKYTM AGARLGSNTL RAGRLNLGTG QYRFPVVGNA KFNTVYILSD ETTPLNIIGC GWEGNYLRRS SGI

UniProtKB: Tail tubular protein gp12

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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

Concentration0.8 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormula
100.0 mMNaCl
10.0 mMMgCl2
50.0 mMTris-HCl

Details: 50 mM Tris-HCl pH 7.8, 100 mM NaCl, 10 mM MgCl2
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
Details: acetone and treated with 0.1% w/v poly-L-Lysine (Sigma) for 1 min in water
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 92382
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6qwp


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6r21:
Cryo-EM structure of T7 bacteriophage fiberless tail complex

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Atomic model buiding 2

Initial modelPDB ID:

5mu4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6r21:
Cryo-EM structure of T7 bacteriophage fiberless tail complex

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Atomic model buiding 3

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6r21:
Cryo-EM structure of T7 bacteriophage fiberless tail complex

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