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- PDB-8fxr: Structure of neck with portal vertex of capsid of Agrobacterium p... -

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Basic information

Entry
Database: PDB / ID: 8fxr
TitleStructure of neck with portal vertex of capsid of Agrobacterium phage Milano
Components
  • (Linking protein ...) x 2
  • Collar sheath protein, gp13
  • Major capsid protein, gp9
  • Minor capsid protein, gp10
  • 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


virion component / viral capsid
Similarity search - Function
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 / : / Phage capsid / Phage capsid family
Similarity search - Domain/homology
Virion-associated protein / Head completion protein / Virion-associated protein / Virion-associated protein / Major capsid 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: 4.5 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
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

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Assembly

Deposited unit
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
a: Neck 1 protein, gp14
b: Neck 1 protein, gp14
l: Neck 1 protein, gp14
n: Neck 1 protein, gp14
o: Neck 1 protein, gp14
p: Neck 1 protein, gp14
q: Neck 1 protein, gp14
h: Neck 1 protein, gp14
i: Neck 1 protein, gp14
j: Neck 1 protein, gp14
k: Neck 1 protein, gp14
m: Neck 1 protein, gp14
H: Neck 2 protein, gp15
I: Neck 2 protein, gp15
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
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
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
AN: Neck 2 protein, gp15
AS: Tail-terminator protein, gp18
AV: Tail-tube, gp21
AT: Tail-terminator protein, gp18
Aa: Tail-tube, gp21
AO: Neck 2 protein, gp15
AW: Tail-terminator protein, gp18
AY: Tail-tube, gp21
AX: Tail-terminator protein, gp18
Ab: Tail-tube, gp21


Theoretical massNumber of molelcules
Total (without water)4,948,734202
Polymers4,948,734202
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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Linking protein ... , 2 types, 30 molecules cdefga1b1d1e1a2b2d2e2a5b5d5e5a6b6d6e6a7b7d7e7f1f2f5f6f7

#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)
#4: 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 , 8 types, 172 molecules ablnopqhijkmHIAMAPANAOg1h1k1n1o1r1g2h2k2n2o2r2...

#2: 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
#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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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

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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: NO / 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10083 / Symmetry type: POINT

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