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- PDB-8fwg: Structure of neck and portal vertex of Agrobacterium phage Milano... -

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Basic information

Entry
Database: PDB / ID: 8fwg
TitleStructure of neck and portal vertex of Agrobacterium phage Milano, C5 symmetry
Components
  • (Linking protein ...) x 2
  • Collar sheath protein, gp13
  • Major capsid protein, gp9
  • Minor capsid protein, gp10
  • Neck 1 protein, gp14
KeywordsVIRUS / Myophage / redox trigger
Function / homologyBacterial Ig domain / Phage capsid / Phage capsid family / Virion-associated protein / Virion-associated protein / Major capsid protein / Virion-associated protein / Head-to-tail connector complex protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 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 22, 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
a1: Linking protein 2, gp128
b1: Linking protein 2, gp128
d1: Linking protein 2, gp128
e1: Linking protein 2, gp128
f1: Linking protein 1, gp16
g1: Major capsid protein, gp9
h1: Major capsid protein, gp9
k1: Major capsid protein, gp9
l1: Minor capsid protein, gp10
m1: Minor capsid protein, gp10
n1: Major capsid protein, gp9
o1: Major capsid protein, gp9
p1: Minor capsid protein, gp10
q1: Minor capsid protein, gp10
r1: Major capsid protein, gp9
s1: Minor capsid protein, gp10
t1: Minor capsid protein, gp10
u1: Minor capsid protein, gp10
v1: Minor capsid protein, gp10
a2: Linking protein 2, gp128
b2: Linking protein 2, gp128
d2: Linking protein 2, gp128
e2: Linking protein 2, gp128
f2: Linking protein 1, gp16
g2: Major capsid protein, gp9
h2: Major capsid protein, gp9
k2: Major capsid protein, gp9
l2: Minor capsid protein, gp10
m2: Minor capsid protein, gp10
n2: Major capsid protein, gp9
o2: Major capsid protein, gp9
p2: Minor capsid protein, gp10
q2: Minor capsid protein, gp10
r2: Major capsid protein, gp9
s2: Minor capsid protein, gp10
t2: Minor capsid protein, gp10
u2: Minor capsid protein, gp10
v2: Minor capsid protein, gp10
J3: Collar sheath protein, gp13
K3: Collar sheath protein, gp13
L3: Collar sheath protein, gp13
M3: Collar sheath protein, gp13
N3: Collar sheath protein, gp13
O3: Collar sheath protein, gp13
P3: Collar sheath protein, gp13
Q3: Collar sheath protein, gp13
R3: Collar sheath protein, gp13
S3: Collar sheath protein, gp13
T3: Collar sheath protein, gp13
U3: Collar sheath protein, gp13
V3: Collar sheath protein, gp13
W3: Collar sheath protein, gp13
X3: Collar sheath protein, gp13
Y3: Collar sheath protein, gp13
Z3: Collar sheath protein, gp13
a3: Collar sheath protein, gp13
b3: Collar sheath protein, gp13
c3: Collar sheath protein, gp13
d3: Collar sheath protein, gp13
e3: Collar sheath protein, gp13
f3: Collar sheath protein, gp13
g3: Collar sheath protein, gp13
h3: Collar sheath protein, gp13
i3: Collar sheath protein, gp13
j3: Collar sheath protein, gp13
k3: Collar sheath protein, gp13
l3: Collar sheath protein, gp13
m3: Collar sheath protein, gp13
n3: Collar sheath protein, gp13
o3: Collar sheath protein, gp13
p3: Collar sheath protein, gp13
q3: Collar sheath protein, gp13
r3: Collar sheath protein, gp13
s3: Collar sheath protein, gp13
t3: Collar sheath protein, gp13
u3: Collar sheath protein, gp13
v3: Collar sheath protein, gp13
w3: Collar sheath protein, gp13
x3: Collar sheath protein, gp13
y3: Collar sheath protein, gp13
z3: Collar sheath protein, gp13
13: Collar sheath protein, gp13
23: Collar sheath protein, gp13
33: Collar sheath protein, gp13
43: Collar sheath protein, gp13
53: Collar sheath protein, gp13
63: Collar sheath protein, gp13
73: Collar sheath protein, gp13
83: Collar sheath protein, gp13
93: Collar sheath protein, gp13
03: Collar sheath protein, gp13
A3: Collar sheath protein, gp13
B3: Collar sheath protein, gp13
C3: Collar sheath protein, gp13
D3: Collar sheath protein, gp13
E3: Collar sheath protein, gp13
F3: Collar sheath protein, gp13
G3: Collar sheath protein, gp13
A4: Neck 1 protein, gp14
B4: Neck 1 protein, gp14
C4: Neck 1 protein, gp14
D4: Neck 1 protein, gp14
E4: Neck 1 protein, gp14
a5: Linking protein 2, gp128
b5: Linking protein 2, gp128
d5: Linking protein 2, gp128
e5: Linking protein 2, gp128
f5: Linking protein 1, gp16
g5: Major capsid protein, gp9
h5: Major capsid protein, gp9
k5: Major capsid protein, gp9
l5: Minor capsid protein, gp10
m5: Minor capsid protein, gp10
n5: Major capsid protein, gp9
o5: Major capsid protein, gp9
p5: Minor capsid protein, gp10
q5: Minor capsid protein, gp10
r5: Major capsid protein, gp9
s5: Minor capsid protein, gp10
t5: Minor capsid protein, gp10
u5: Minor capsid protein, gp10
v5: Minor capsid protein, gp10
a6: Linking protein 2, gp128
b6: Linking protein 2, gp128
d6: Linking protein 2, gp128
e6: Linking protein 2, gp128
f6: Linking protein 1, gp16
g6: Major capsid protein, gp9
h6: Major capsid protein, gp9
k6: Major capsid protein, gp9
l6: Minor capsid protein, gp10
m6: Minor capsid protein, gp10
n6: Major capsid protein, gp9
o6: Major capsid protein, gp9
p6: Minor capsid protein, gp10
q6: Minor capsid protein, gp10
r6: Major capsid protein, gp9
s6: Minor capsid protein, gp10
t6: Minor capsid protein, gp10
u6: Minor capsid protein, gp10
v6: Minor capsid protein, gp10
a7: Linking protein 2, gp128
b7: Linking protein 2, gp128
d7: Linking protein 2, gp128
e7: Linking protein 2, gp128
f7: Linking protein 1, gp16
g7: Major capsid protein, gp9
h7: Major capsid protein, gp9
k7: Major capsid protein, gp9
l7: Minor capsid protein, gp10
m7: Minor capsid protein, gp10
n7: Major capsid protein, gp9
o7: Major capsid protein, gp9
p7: Minor capsid protein, gp10
q7: Minor capsid protein, gp10
r7: Major capsid protein, gp9
s7: Minor capsid protein, gp10
t7: Minor capsid protein, gp10
u7: Minor capsid protein, gp10
v7: Minor capsid protein, gp10
c: Linking protein 2, gp128
d: Linking protein 2, gp128
e: Linking protein 2, gp128
f: Linking protein 2, gp128
g: Linking protein 2, gp128


Theoretical massNumber of molelcules
Total (without water)3,936,890165
Polymers3,936,890165
Non-polymers00
Water0
1


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

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Components

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Linking protein ... , 2 types, 30 molecules a1b1d1e1a2b2d2e2a5b5d5e5a6b6d6e6a7b7d7e7cdefgf1f2f5f6f7

#1: Protein/peptide ...
Linking protein 2, gp128


Mass: 3942.762 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus)
#2: Protein
Linking protein 1, gp16


Mass: 22913.605 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFR0

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Protein , 4 types, 135 molecules g1h1k1n1o1r1g2h2k2n2o2r2g5h5k5n5o5r5g6h6k6n6o6r6g7h7k7n7o7r7...

#3: Protein ...
Major capsid protein, gp9


Mass: 52037.324 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS6
#4: Protein ...
Minor capsid protein, gp10


Mass: 14548.290 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS0
#5: Protein ...
Collar sheath protein, gp13


Mass: 24490.402 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MGH3
#6: Protein
Neck 1 protein, gp14


Mass: 22255.439 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHL8

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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: all / 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 FIELDBright-field microscopy / 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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10086 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005227095
ELECTRON MICROSCOPYf_angle_d0.697309610
ELECTRON MICROSCOPYf_dihedral_angle_d7.47132925
ELECTRON MICROSCOPYf_chiral_restr0.04934000
ELECTRON MICROSCOPYf_plane_restr0.00541170

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