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- PDB-6qzf: The cryo-EM structure of the collar complex and tail axis in geno... -

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Basic information

Entry
Database: PDB / ID: 6qzf
TitleThe cryo-EM structure of the collar complex and tail axis in genome emptied bacteriophage phi29
Components
  • Portal protein
  • Pre-neck appendage protein
  • Proximal tail tube connector protein
KeywordsVIRUS / bacteriophage / phi29 / genome emptied virion
Function / homology
Function and homology information


disruption of host cell envelope during viral entry / virus tail, tube / viral portal complex / viral DNA genome packaging / viral genome ejection through host cell envelope, short tail mechanism / viral procapsid / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding ...disruption of host cell envelope during viral entry / virus tail, tube / viral portal complex / viral DNA genome packaging / viral genome ejection through host cell envelope, short tail mechanism / viral procapsid / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / RNA binding / ATP binding / metal ion binding
Parallel beta-helix repeat / Phage Connector (GP10) / Pectate lyase superfamily protein / Peptidase G2, IMC autoproteolytic cleavage domain / Pectin lyase fold / Pectin lyase fold/virulence factor / Portal protein Gp10 / Peptidase_G2, IMC autoproteolytic cleavage domain / Portal protein Gp10 superfamily / Pectate lyase superfamily protein
Portal protein / Pre-neck appendage protein / Proximal tail tube connector protein
Biological speciesBacillus phage phi29 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXu, J. / Wang, D. / Gui, M. / Xiang, Y.
Funding supportChina , 3件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100China
Ministry of Science and Technology (China)2015CB910102China
National Natural Science Foundation of China31470721China
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 11, 2019 / Release: Jun 12, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release
1.1Jun 19, 2019Structure modelData collection / Structure summaryem_admin / pdbx_database_proc / struct_em_admin.last_update / _em_admin.title / _struct.title

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Structure viewerMolecule:
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Assembly

Deposited unit
0a: Portal protein
0b: Portal protein
0c: Portal protein
0d: Portal protein
0e: Portal protein
0f: Portal protein
0g: Portal protein
0h: Portal protein
0i: Portal protein
0j: Portal protein
0k: Portal protein
0l: Portal protein
0A: Proximal tail tube connector protein
0B: Proximal tail tube connector protein
0C: Proximal tail tube connector protein
0D: Proximal tail tube connector protein
0E: Proximal tail tube connector protein
0F: Proximal tail tube connector protein
0G: Proximal tail tube connector protein
0H: Proximal tail tube connector protein
0I: Proximal tail tube connector protein
0J: Proximal tail tube connector protein
0K: Proximal tail tube connector protein
0L: Proximal tail tube connector protein
A: Pre-neck appendage protein
B: Pre-neck appendage protein
C: Pre-neck appendage protein
D: Pre-neck appendage protein
E: Pre-neck appendage protein
F: Pre-neck appendage protein
G: Pre-neck appendage protein
H: Pre-neck appendage protein
I: Pre-neck appendage protein
J: Pre-neck appendage protein
K: Pre-neck appendage protein
L: Pre-neck appendage protein
M: Pre-neck appendage protein
N: Pre-neck appendage protein
O: Pre-neck appendage protein
P: Pre-neck appendage protein
Q: Pre-neck appendage protein
R: Pre-neck appendage protein
S: Pre-neck appendage protein
T: Pre-neck appendage protein
U: Pre-neck appendage protein
V: Pre-neck appendage protein
W: Pre-neck appendage protein
X: Pre-neck appendage protein
Y: Pre-neck appendage protein
Z: Pre-neck appendage protein
a: Pre-neck appendage protein
b: Pre-neck appendage protein
c: Pre-neck appendage protein
d: Pre-neck appendage protein
e: Pre-neck appendage protein
f: Pre-neck appendage protein
g: Pre-neck appendage protein
h: Pre-neck appendage protein
i: Pre-neck appendage protein
j: Pre-neck appendage protein


Theoretical massNumber of molelcules
Total (without water)4,156,04360
Polymers4,156,04360
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Portal protein / Connector protein / Gene product 10 / gp10 / Gene product 19 / gp19 / Head-to-tail connector / Probable portal protein / Protein p10 / Upper collar protein


Mass: 35917.293 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (bacteriophage) / References: UniProt: P04332
#2: Protein/peptide
Proximal tail tube connector protein / Gene product 11 / gp11 / Lower collar protein / Protein p11


Mass: 33839.086 Da / Num. of mol.: 12
Details: the residues from 170 to 191 are assigned poly-alanine due to poor quality of map
Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (bacteriophage) / References: UniProt: P68930
#3: Protein/peptide ...
Pre-neck appendage protein / Gene product 12 / gp12 / NP1 / Protein p12


Mass: 92193.523 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (bacteriophage) / References: UniProt: P20345

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus phage phi29 / Type: VIRUS / Entity ID: 1,2,3 / Source: NATURAL
Source (natural)Organism: Bacillus phage phi29 (bacteriophage)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: PRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31478 / Symmetry type: POINT

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