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- PDB-8i4m: Portal-tail complex structure of the Cyanophage P-SCSP1u -

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Basic information

Entry
Database: PDB / ID: 8i4m
TitlePortal-tail complex structure of the Cyanophage P-SCSP1u
Components
  • Adaptor protein(gp22) of the cyanophage P-SCSP1uAdapter
  • Fiber protein(gp 28) of the cyanophage P-SCSP1u
  • Nozzle protein(gp 23) of the cyanophage P-SCSP1u
  • Portal protein(gp 16) of the cyanophage P-SCSP1u
KeywordsVIRUS / Whole virus / Capsid / cyanophage / T7-like virus
Biological speciesProchlorococcus phage P-SCSP1u (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsLiu, H. / Dang, S.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses.
Authors: Lanlan Cai / Hang Liu / Wen Zhang / Shiwei Xiao / Qinglu Zeng / Shangyu Dang /
Abstract: Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria ...Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses.
History
DepositionJan 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Portal protein(gp 16) of the cyanophage P-SCSP1u
T: Portal protein(gp 16) of the cyanophage P-SCSP1u
U: Portal protein(gp 16) of the cyanophage P-SCSP1u
V: Portal protein(gp 16) of the cyanophage P-SCSP1u
W: Portal protein(gp 16) of the cyanophage P-SCSP1u
X: Portal protein(gp 16) of the cyanophage P-SCSP1u
Y: Portal protein(gp 16) of the cyanophage P-SCSP1u
Z: Portal protein(gp 16) of the cyanophage P-SCSP1u
a: Portal protein(gp 16) of the cyanophage P-SCSP1u
b: Portal protein(gp 16) of the cyanophage P-SCSP1u
c: Portal protein(gp 16) of the cyanophage P-SCSP1u
d: Portal protein(gp 16) of the cyanophage P-SCSP1u
A: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
B: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
C: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
D: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
E: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
F: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
G: Adaptor protein(gp22) of the cyanophage P-SCSP1u
H: Adaptor protein(gp22) of the cyanophage P-SCSP1u
I: Adaptor protein(gp22) of the cyanophage P-SCSP1u
J: Adaptor protein(gp22) of the cyanophage P-SCSP1u
K: Adaptor protein(gp22) of the cyanophage P-SCSP1u
L: Adaptor protein(gp22) of the cyanophage P-SCSP1u
q: Adaptor protein(gp22) of the cyanophage P-SCSP1u
r: Adaptor protein(gp22) of the cyanophage P-SCSP1u
s: Adaptor protein(gp22) of the cyanophage P-SCSP1u
t: Adaptor protein(gp22) of the cyanophage P-SCSP1u
u: Adaptor protein(gp22) of the cyanophage P-SCSP1u
v: Adaptor protein(gp22) of the cyanophage P-SCSP1u
e: Fiber protein(gp 28) of the cyanophage P-SCSP1u
f: Fiber protein(gp 28) of the cyanophage P-SCSP1u
g: Fiber protein(gp 28) of the cyanophage P-SCSP1u
h: Fiber protein(gp 28) of the cyanophage P-SCSP1u
j: Fiber protein(gp 28) of the cyanophage P-SCSP1u
l: Fiber protein(gp 28) of the cyanophage P-SCSP1u
i: Fiber protein(gp 28) of the cyanophage P-SCSP1u
k: Fiber protein(gp 28) of the cyanophage P-SCSP1u
m: Fiber protein(gp 28) of the cyanophage P-SCSP1u
n: Fiber protein(gp 28) of the cyanophage P-SCSP1u
o: Fiber protein(gp 28) of the cyanophage P-SCSP1u
p: Fiber protein(gp 28) of the cyanophage P-SCSP1u
M: Fiber protein(gp 28) of the cyanophage P-SCSP1u
N: Fiber protein(gp 28) of the cyanophage P-SCSP1u
O: Fiber protein(gp 28) of the cyanophage P-SCSP1u
P: Fiber protein(gp 28) of the cyanophage P-SCSP1u
Q: Fiber protein(gp 28) of the cyanophage P-SCSP1u
R: Fiber protein(gp 28) of the cyanophage P-SCSP1u


Theoretical massNumber of molelcules
Total (without water)3,597,35148
Polymers3,597,35148
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Portal protein(gp 16) of the cyanophage P-SCSP1u


Mass: 62460.434 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus phage P-SCSP1u (virus)
#2: Protein
Nozzle protein(gp 23) of the cyanophage P-SCSP1u


Mass: 87444.898 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus phage P-SCSP1u (virus)
#3: Protein
Adaptor protein(gp22) of the cyanophage P-SCSP1u / Adapter


Mass: 22811.480 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus phage P-SCSP1u (virus)
#4: Protein
Fiber protein(gp 28) of the cyanophage P-SCSP1u /


Mass: 113856.602 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Prochlorococcus phage P-SCSP1u (virus)
Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Prochlorococcus phage P-SCSP1uVIRUS#2-#3, #1, #40NATURAL
2The portal-tail complex of cyanophage P-SCSP1uCOMPLEX#2-#4, #11NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Prochlorococcus phage P-SCSP1u (virus)2914505
32Prochlorococcus phage P-SCSP1u (virus)2914505
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Prochlorococcus
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisitionThe EPU was used to automatically collect images.
4cryoSPARC2.15CTF correction
10cryoSPARC2.15initial Euler assignment
11cryoSPARC2.15final Euler assignment
12RELION3.1classification
13cryoSPARC2.15classification
14cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86469 / Symmetry type: POINT
Atomic model buildingDetails: the initial model of our models was predicted by the alpha fold according to the protein sequence.

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