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- EMDB-4685: The cryo-EM structure of the collar complex and tail axis in geno... -

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Basic information

Entry
Database: EMDB / ID: EMD-4685
TitleThe cryo-EM structure of the collar complex and tail axis in genome emptied bacteriophage phi29
Map data
Sample
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Proximal tail tube connector protein
    • Protein or peptide: Pre-neck appendage protein
Keywordsbacteriophage / phi29 / genome emptied virion / VIRUS
Function / homology
Function and homology information


virus tail, tube / viral portal complex / viral procapsid / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding ...virus tail, tube / viral portal complex / viral procapsid / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Portal protein / Pre-neck appendage protein / Proximal tail tube connector protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXu J / Wang D
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910102 China
National Natural Science Foundation of China31470721 China
CitationJournal: Nat Commun / Year: 2019
Title: Structural assembly of the tailed bacteriophage ϕ29.
Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang /
Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.
History
DepositionMar 11, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qzf
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qzf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4685.png

Downloads & links

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Map

FileDownload / File: emd_4685.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 540 pix.
= 734.4 Å		1.36 Å/pix.
x 540 pix.
= 734.4 Å		1.36 Å/pix.
x 540 pix.
= 734.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-4.8601074 - 22.011310000000002
Average (Standard dev.)0.00010756623 (±0.23255783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 734.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z734.400734.400734.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-4.86022.0110.000

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Supplemental data

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Sample components

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Entire : Bacillus phage phi29

EntireName: Bacillus phage phi29 (virus)
Components
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Proximal tail tube connector protein
    • Protein or peptide: Pre-neck appendage protein

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Virus type: PRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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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: Bacillus phage phi29 (virus)
Molecular weightTheoretical: 35.917293 KDa
SequenceString: MARKRSNTYR SINEIQRQKR NRWFIHYLNY LQSLAYQLFE WENLPPTINP SFLEKSIHQF GYVGFYKDPV ISYIACNGAL SGQRDVYNQ ATVFRAASPV YQKEFKLYNY RDMKEEDMGV VIYNNDMAFP TTPTLELFAA ELAELKEIIS VNQNAQKTPV L IRANDNNQ ...String:
MARKRSNTYR SINEIQRQKR NRWFIHYLNY LQSLAYQLFE WENLPPTINP SFLEKSIHQF GYVGFYKDPV ISYIACNGAL SGQRDVYNQ ATVFRAASPV YQKEFKLYNY RDMKEEDMGV VIYNNDMAFP TTPTLELFAA ELAELKEIIS VNQNAQKTPV L IRANDNNQ LSLKQVYNQY EGNAPVIFAH EALDSDSIEV FKTDAPYVVD KLNAQKNAVW NEMMTFLGIK NANLEKKERM VT DEVSSND EQIESSGTVF LKSREEACEK INELYGLNVK VKFRYDIVEQ MRRELQQIEN VSRGTSDGET NE

UniProtKB: Portal protein

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Macromolecule #2: Proximal tail tube connector protein

MacromoleculeName: Proximal tail tube connector protein / type: protein_or_peptide / ID: 2
Details: the residues from 170 to 191 are assigned poly-alanine due to poor quality of map
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage phi29 (virus)
Molecular weightTheoretical: 33.839086 KDa
SequenceString: MSSYTMQLRT YIEMWSQGET GLSTAEKIEK GRPKLFDFNY PIFDESYRTI FETHFIRNFY MREIGFETEG LFKFHLETWL MINMPYFNK LFESELIKYD PLENTRVGVK SNTKNDTDRN DNRDVKQDLT SNGTSSTDAK QNDTSKTTGN EKSSGSGSIT D DNFKRDLN ...String:
MSSYTMQLRT YIEMWSQGET GLSTAEKIEK GRPKLFDFNY PIFDESYRTI FETHFIRNFY MREIGFETEG LFKFHLETWL MINMPYFNK LFESELIKYD PLENTRVGVK SNTKNDTDRN DNRDVKQDLT SNGTSSTDAK QNDTSKTTGN EKSSGSGSIT D DNFKRDLN ADTADDRLQL TTKDGEGVLE YASQIEEHNE NKKRDTKTSN TTDTTSNTTG TSTLDSDSKT SNKANTTSND KL NSQINSV EDYIEDRVGK IGTQSYARLV MDYREALLRI EQRIFNEMQE LFMLVY

UniProtKB: Proximal tail tube connector protein

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Macromolecule #3: Pre-neck appendage protein

MacromoleculeName: Pre-neck appendage protein / type: protein_or_peptide / ID: 3 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage phi29 (virus)
Molecular weightTheoretical: 92.193523 KDa
SequenceString: MSTKPELKRF EQFGEMMVQL YERYLPTAFD ESLTLLEKMN KIIHYLNEIG KVTNELIEEW NKVMEWILND GLEDLVKETL ERWYEEGKF ADLVIQVIDE LKQFGVSVKT YGAKGDGVTD DIRAFEKAIE SGFPVYVPYG TFMVSRGIKL PSNTVLTGAG K RNAVIKFM ...String:
MSTKPELKRF EQFGEMMVQL YERYLPTAFD ESLTLLEKMN KIIHYLNEIG KVTNELIEEW NKVMEWILND GLEDLVKETL ERWYEEGKF ADLVIQVIDE LKQFGVSVKT YGAKGDGVTD DIRAFEKAIE SGFPVYVPYG TFMVSRGIKL PSNTVLTGAG K RNAVIKFM DSVGRGESLM YNQNVTTGNE NIFLSSFTLD GNNKRLGQGI SGIGGSRESN LSIRACHNVY IRDIEAVDCT LH GIDITCG GLDYPYLGDG TTAPNPSENI WIENCEATGF GDDGITTHHS QYINILNCYS HDPRLTANCN GFEIDDGSRH VVL SNNRSK GCYGGIEIKA HGDAPAAYNI SINGHMSVED VRSYNFRHIG HHAATDPQSV SAKNIVASNL VSIRPNNKRG FQDN ATPRV LAVSAYYGVV INGLTGYTDD PNLLTETVVS VQFRARNCSL NGVGLTGFSN SDNGIYVIGG SRGGDAVNIS NVTLN NSGR YGVSIGSGIE NVSITNISGI GDGINSPVAL VSTINSNPEI SGLSSIGYPT AARVAGTDYN DGLTLFNGAF RASTTS SGK IHSEGFIMGS TSGCEASVSK SGVLTSSSSK TSSERSLIAG SSTSEAKGTY NTILGSLGAV ADEQFAALIS ASQSRAS GN HNLILSSYGI NTTGSYKVNG GFEKINWELD SLNGRIKARD TVTGGNTWSD FAEYFESLDG QVIETGYLVT LEKGKIRK A EKGEKIIGVI SETAGFVLGE SSFEWQGAVL KNEFGGIIYE EVTTEDGVKF KRPLPSPDFD PNKNYIPRSQ RREWHVVGL LGQIAVRIDE TVKQGHGIDA VGGVATDGDN FIVQEITTPY TKEKGYGVAI VLVK

UniProtKB: Pre-neck appendage 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 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: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31478
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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