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- PDB-8fwe: Neck structure of Agrobacterium phage Milano, C3 symmetry -

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Basic information

Entry
Database: PDB / ID: 8fwe
TitleNeck structure of Agrobacterium phage Milano, C3 symmetry
Components
  • Collar sheath protein, gp13
  • Neck 1 protein, gp14
  • Neck 2 protein, gp15
  • Portal protein, gp7
  • Tail-terminator protein, gp18
  • Tail-tube, gp21
KeywordsVIRUS / Myophage / redox trigger
Function / homology
Function and homology information


Bacterial Ig domain / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage SPP1, head-tail adaptor / Phage head completion protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein
Similarity search - Domain/homology
Virion-associated protein / Head completion protein / Portal protein / Virion-associated protein / Virion-associated protein / Head-to-tail connector complex protein
Similarity search - Component
Biological speciesAgrobacterium phage Milano (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 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 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Collar sheath protein, gp13
K: Collar sheath protein, gp13
L: Collar sheath protein, gp13
M: Collar sheath protein, gp13
N: Collar sheath protein, gp13
O: Collar sheath protein, gp13
P: Collar sheath protein, gp13
Q: Collar sheath protein, gp13
R: Collar sheath protein, gp13
S: Collar sheath protein, gp13
T: Collar sheath protein, gp13
U: Collar sheath protein, gp13
V: Collar sheath protein, gp13
W: Collar sheath protein, gp13
X: Collar sheath protein, gp13
Y: Collar sheath protein, gp13
Z: Collar sheath protein, gp13
a: Collar sheath protein, gp13
b: Collar sheath protein, gp13
c: Collar sheath protein, gp13
d: Collar sheath protein, gp13
e: Collar sheath protein, gp13
f: Collar sheath protein, gp13
g: Collar sheath protein, gp13
h: Collar sheath protein, gp13
i: Collar sheath protein, gp13
j: Collar sheath protein, gp13
k: Collar sheath protein, gp13
l: Collar sheath protein, gp13
m: Collar sheath protein, gp13
n: Collar sheath protein, gp13
o: Collar sheath protein, gp13
p: Collar sheath protein, gp13
q: Collar sheath protein, gp13
r: Collar sheath protein, gp13
s: Collar sheath protein, gp13
t: Collar sheath protein, gp13
u: Collar sheath protein, gp13
v: Collar sheath protein, gp13
w: Collar sheath protein, gp13
x: Collar sheath protein, gp13
y: Collar sheath protein, gp13
z: Collar sheath protein, gp13
1: Collar sheath protein, gp13
2: Collar sheath protein, gp13
3: Collar sheath protein, gp13
4: Collar sheath protein, gp13
5: Collar sheath protein, gp13
6: Collar sheath protein, gp13
7: Collar sheath protein, gp13
8: Collar sheath protein, gp13
9: Collar sheath protein, gp13
0: Collar sheath protein, gp13
A: Collar sheath protein, gp13
B: Collar sheath protein, gp13
C: Collar sheath protein, gp13
D: Collar sheath protein, gp13
E: Collar sheath protein, gp13
F: Collar sheath protein, gp13
G: Collar sheath protein, gp13
AA: Portal protein, gp7
AB: Portal protein, gp7
AC: Portal protein, gp7
AD: Portal protein, gp7
AE: Portal protein, gp7
AF: Portal protein, gp7
AG: Portal protein, gp7
AH: Portal protein, gp7
AI: Portal protein, gp7
AJ: Portal protein, gp7
AK: Portal protein, gp7
AL: Portal protein, gp7
AM: Neck 2 protein, gp15
AQ: Tail-terminator protein, gp18
AU: Tail-tube, gp21
AR: Tail-terminator protein, gp18
AP: Neck 2 protein, gp15
AZ: Tail-tube, gp21
R3: Neck 1 protein, gp14
S3: Neck 1 protein, gp14
T3: Neck 1 protein, gp14
U3: Neck 1 protein, gp14
AN: Neck 2 protein, gp15
AS: Tail-terminator protein, gp18
AV: Tail-tube, gp21
AT: Tail-terminator protein, gp18
H: Neck 2 protein, gp15
Aa: Tail-tube, gp21
R4: Neck 1 protein, gp14
S4: Neck 1 protein, gp14
T4: Neck 1 protein, gp14
U4: Neck 1 protein, gp14
AO: Neck 2 protein, gp15
AW: Tail-terminator protein, gp18
AY: Tail-tube, gp21
AX: Tail-terminator protein, gp18
I: Neck 2 protein, gp15
Ab: Tail-tube, gp21
R5: Neck 1 protein, gp14
S5: Neck 1 protein, gp14
T5: Neck 1 protein, gp14
U5: Neck 1 protein, gp14


Theoretical massNumber of molelcules
Total (without water)2,592,545102
Polymers2,592,545102
Non-polymers00
Water00
1


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

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Components

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Protein , 6 types, 102 molecules JKLMNOPQRSTUVWXYZabcdefghijklm...

#1: 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
#2: Protein
Portal protein, gp7


Mass: 45840.844 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFW7
#3: Protein
Neck 2 protein, gp15


Mass: 16052.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFQ3
#4: Protein
Tail-terminator protein, gp18


Mass: 20268.541 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MF73
#5: Protein
Tail-tube, gp21


Mass: 14673.427 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHE7
#6: Protein
Neck 1 protein, gp14


Mass: 22255.439 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHL8

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Details

Has protein modificationY

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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 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
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10216 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011176070
ELECTRON MICROSCOPYf_angle_d0.832239802
ELECTRON MICROSCOPYf_dihedral_angle_d7.04104466
ELECTRON MICROSCOPYf_chiral_restr0.05226718
ELECTRON MICROSCOPYf_plane_restr0.00631722

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