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- PDB-8fxp: Structure of capsid of Agrobacterium phage Milano -

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Basic information

Entry
Database: PDB / ID: 8fxp
TitleStructure of capsid of Agrobacterium phage Milano
Components
  • Linking protein 1, gp16
  • Linking protein 2, gp128
  • Major capsid protein, gp9
  • Minor capsid protein, gp10
KeywordsVIRUS / Myophage / redox trigger
Function / homologyPhage capsid / Phage capsid family / Virion-associated protein / Virion-associated protein / Major capsid protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsSonani, R.R. / Wang, F. / Esteves, N.C. / Kelly, R.J. / Sebastian, A. / Kreutzberger, M.A.B. / Leiman, P.G. / Scharf, B.E. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Commun Biol / Year: 2023
Title: Neck and capsid architecture of the robust Agrobacterium phage Milano.
Authors: Ravi R Sonani / Nathaniel C Esteves / Abigail A Horton / Rebecca J Kelly / Amanda L Sebastian / Fengbin Wang / Mark A B Kreutzberger / Petr G Leiman / Birgit E Scharf / Edward H Egelman /
Abstract: Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is ...Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Linking protein 1, gp16
1: Minor capsid protein, gp10
2: Minor capsid protein, gp10
3: Minor capsid protein, gp10
4: Minor capsid protein, gp10
5: Minor capsid protein, gp10
6: Minor capsid protein, gp10
7: Minor capsid protein, gp10
8: Minor capsid protein, gp10
9: Minor capsid protein, gp10
a: Linking protein 2, gp128
b: Linking protein 2, gp128
c: Linking protein 2, gp128
d: Linking protein 2, gp128
e: Linking protein 2, gp128
f: Linking protein 1, gp16
g: Major capsid protein, gp9
h: Major capsid protein, gp9
i: Major capsid protein, gp9
j: Major capsid protein, gp9
k: Major capsid protein, gp9
l: Minor capsid protein, gp10
m: Minor capsid protein, gp10
n: Major capsid protein, gp9
o: Major capsid protein, gp9
p: Minor capsid protein, gp10
q: Minor capsid protein, gp10
r: Major capsid protein, gp9
s: Minor capsid protein, gp10
t: Minor capsid protein, gp10
u: Minor capsid protein, gp10
v: Minor capsid protein, gp10
w: Major capsid protein, gp9
x: Major capsid protein, gp9
y: Major capsid protein, gp9
z: Minor capsid protein, gp10
0A: Linking protein 1, gp16
0B: Linking protein 1, gp16
0C: Linking protein 1, gp16
0D: Linking protein 1, gp16
0E: Minor capsid protein, gp10
0F: Minor capsid protein, gp10
AA: Major capsid protein, gp9
AB: Major capsid protein, gp9
AC: Major capsid protein, gp9
AD: Minor capsid protein, gp10
AE: Minor capsid protein, gp10
AF: Major capsid protein, gp9
AG: Major capsid protein, gp9
AH: Minor capsid protein, gp10
AI: Minor capsid protein, gp10
AJ: Major capsid protein, gp9
AK: Minor capsid protein, gp10
AL: Minor capsid protein, gp10
AM: Minor capsid protein, gp10
AN: Minor capsid protein, gp10
0G: Minor capsid protein, gp10
0H: Minor capsid protein, gp10
AO: Linking protein 2, gp128
AP: Linking protein 2, gp128
AR: Linking protein 2, gp128
AS: Linking protein 2, gp128
AQ: Linking protein 2, gp128
AT: Linking protein 2, gp128


Theoretical massNumber of molelcules
Total (without water)1,501,93564
Polymers1,501,93564
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Linking protein 1, gp16


Mass: 22913.605 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFR0
#2: Protein ...
Minor capsid protein, gp10


Mass: 14548.290 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS0
#3: Protein/peptide
Linking protein 2, gp128


Mass: 3942.762 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus)
#4: Protein
Major capsid protein, gp9


Mass: 52037.324 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS6

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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: Agrobacterium phage Milano / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Agrobacterium phage Milano (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Agrobacterium fabrum str. C58
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15740 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01175023
ELECTRON MICROSCOPYf_angle_d0.751102154
ELECTRON MICROSCOPYf_dihedral_angle_d8.16743854
ELECTRON MICROSCOPYf_chiral_restr0.04611125
ELECTRON MICROSCOPYf_plane_restr0.00513605

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