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- PDB-8fqc: Structure of baseplate with receptor binding complex of Agrobacte... -

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Basic information

Entry
Database: PDB / ID: 8fqc
TitleStructure of baseplate with receptor binding complex of Agrobacterium phage Milano
Components
  • (Baseplate Wedge ...) x 3
  • Baseplate Centerpiece, gp25
  • Baseplate Central Spike, gp27
  • Baseplate hub protein, gp26
  • Short Tail Fibers, gp31
  • Tail Spike protein, gp124
  • Tail sheath protein, gp20
  • Tail-tube, gp21
KeywordsVIRUS / Myophage / redox trigger / disulfides
Function / homology
Function and homology information


DNA circulation, N-terminal / DNA circularisation protein N-terminus / Baseplate protein J-like / Baseplate J-like protein / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
: / DNA-circularization protein / Baseplate hub protein / Tail sheath protein / Virion-associated protein / Baseplate protein / Baseplate protein / Tail fiber protein / Virion-associated protein / Virion-associated protein
Similarity search - Component
Biological speciesAgrobacterium phage Milano (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSonani, R.R. / Leiman, P.G. / Wang, F. / Kreutzberger, M.A.B. / Sebastian, A. / Esteves, N.C. / Kelly, R.J. / Scharf, B. / 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: Nat Commun / Year: 2024
Title: An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.
Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / ...Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / Birgit E Scharf / Edward H Egelman /
Abstract: A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, ...A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
History
DepositionJan 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C1: Baseplate hub protein, gp26
E1: Tail-tube, gp21
F1: Baseplate Wedge 2 protein, gp29
G1: Baseplate Wedge 2 protein, gp29
H1: Baseplate wedge 1, gp28
I1: Tail sheath protein, gp20
J1: Baseplate Wedge 3 protein, gp30
K1: Tail sheath protein, gp20
P1: Tail Spike protein, gp124
Q1: Tail Spike protein, gp124
R1: Tail Spike protein, gp124
S1: Short Tail Fibers, gp31
T1: Short Tail Fibers, gp31
U1: Baseplate Centerpiece, gp25
V1: Short Tail Fibers, gp31
W1: Short Tail Fibers, gp31
X1: Short Tail Fibers, gp31
Y1: Short Tail Fibers, gp31
a1: Tail-tube, gp21
e1: Baseplate Centerpiece, gp25
f1: Tail-tube, gp21
g1: Tail-tube, gp21
h1: Baseplate Wedge 2 protein, gp29
i1: Baseplate Wedge 2 protein, gp29
j1: Baseplate wedge 1, gp28
k1: Tail sheath protein, gp20
l1: Baseplate Wedge 3 protein, gp30
m1: Tail sheath protein, gp20
r1: Tail Spike protein, gp124
s1: Tail Spike protein, gp124
t1: Tail Spike protein, gp124
v1: Short Tail Fibers, gp31
w1: Short Tail Fibers, gp31
x1: Short Tail Fibers, gp31
y1: Short Tail Fibers, gp31
u1: Short Tail Fibers, gp31
z1: Short Tail Fibers, gp31
A: Baseplate Central Spike, gp27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,455,99939
Polymers1,455,94338
Non-polymers561
Water0
1
C1: Baseplate hub protein, gp26
E1: Tail-tube, gp21
F1: Baseplate Wedge 2 protein, gp29
G1: Baseplate Wedge 2 protein, gp29
H1: Baseplate wedge 1, gp28
I1: Tail sheath protein, gp20
J1: Baseplate Wedge 3 protein, gp30
K1: Tail sheath protein, gp20
P1: Tail Spike protein, gp124
Q1: Tail Spike protein, gp124
R1: Tail Spike protein, gp124
S1: Short Tail Fibers, gp31
T1: Short Tail Fibers, gp31
U1: Baseplate Centerpiece, gp25
V1: Short Tail Fibers, gp31
W1: Short Tail Fibers, gp31
X1: Short Tail Fibers, gp31
Y1: Short Tail Fibers, gp31
a1: Tail-tube, gp21
e1: Baseplate Centerpiece, gp25
f1: Tail-tube, gp21
g1: Tail-tube, gp21
h1: Baseplate Wedge 2 protein, gp29
i1: Baseplate Wedge 2 protein, gp29
j1: Baseplate wedge 1, gp28
k1: Tail sheath protein, gp20
l1: Baseplate Wedge 3 protein, gp30
m1: Tail sheath protein, gp20
r1: Tail Spike protein, gp124
s1: Tail Spike protein, gp124
t1: Tail Spike protein, gp124
v1: Short Tail Fibers, gp31
w1: Short Tail Fibers, gp31
x1: Short Tail Fibers, gp31
y1: Short Tail Fibers, gp31
u1: Short Tail Fibers, gp31
z1: Short Tail Fibers, gp31
A: Baseplate Central Spike, gp27
hetero molecules

C1: Baseplate hub protein, gp26
E1: Tail-tube, gp21
F1: Baseplate Wedge 2 protein, gp29
G1: Baseplate Wedge 2 protein, gp29
H1: Baseplate wedge 1, gp28
I1: Tail sheath protein, gp20
J1: Baseplate Wedge 3 protein, gp30
K1: Tail sheath protein, gp20
P1: Tail Spike protein, gp124
Q1: Tail Spike protein, gp124
R1: Tail Spike protein, gp124
S1: Short Tail Fibers, gp31
T1: Short Tail Fibers, gp31
U1: Baseplate Centerpiece, gp25
V1: Short Tail Fibers, gp31
W1: Short Tail Fibers, gp31
X1: Short Tail Fibers, gp31
Y1: Short Tail Fibers, gp31
a1: Tail-tube, gp21
e1: Baseplate Centerpiece, gp25
f1: Tail-tube, gp21
g1: Tail-tube, gp21
h1: Baseplate Wedge 2 protein, gp29
i1: Baseplate Wedge 2 protein, gp29
j1: Baseplate wedge 1, gp28
k1: Tail sheath protein, gp20
l1: Baseplate Wedge 3 protein, gp30
m1: Tail sheath protein, gp20
r1: Tail Spike protein, gp124
s1: Tail Spike protein, gp124
t1: Tail Spike protein, gp124
v1: Short Tail Fibers, gp31
w1: Short Tail Fibers, gp31
x1: Short Tail Fibers, gp31
y1: Short Tail Fibers, gp31
u1: Short Tail Fibers, gp31
z1: Short Tail Fibers, gp31
A: Baseplate Central Spike, gp27
hetero molecules

C1: Baseplate hub protein, gp26
E1: Tail-tube, gp21
F1: Baseplate Wedge 2 protein, gp29
G1: Baseplate Wedge 2 protein, gp29
H1: Baseplate wedge 1, gp28
I1: Tail sheath protein, gp20
J1: Baseplate Wedge 3 protein, gp30
K1: Tail sheath protein, gp20
P1: Tail Spike protein, gp124
Q1: Tail Spike protein, gp124
R1: Tail Spike protein, gp124
S1: Short Tail Fibers, gp31
T1: Short Tail Fibers, gp31
U1: Baseplate Centerpiece, gp25
V1: Short Tail Fibers, gp31
W1: Short Tail Fibers, gp31
X1: Short Tail Fibers, gp31
Y1: Short Tail Fibers, gp31
a1: Tail-tube, gp21
e1: Baseplate Centerpiece, gp25
f1: Tail-tube, gp21
g1: Tail-tube, gp21
h1: Baseplate Wedge 2 protein, gp29
i1: Baseplate Wedge 2 protein, gp29
j1: Baseplate wedge 1, gp28
k1: Tail sheath protein, gp20
l1: Baseplate Wedge 3 protein, gp30
m1: Tail sheath protein, gp20
r1: Tail Spike protein, gp124
s1: Tail Spike protein, gp124
t1: Tail Spike protein, gp124
v1: Short Tail Fibers, gp31
w1: Short Tail Fibers, gp31
x1: Short Tail Fibers, gp31
y1: Short Tail Fibers, gp31
u1: Short Tail Fibers, gp31
z1: Short Tail Fibers, gp31
A: Baseplate Central Spike, gp27
hetero molecules


  • complete point assembly
  • 4.37 MDa, 114 polymers
Theoretical massNumber of molelcules
Total (without water)4,367,997117
Polymers4,367,829114
Non-polymers1683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

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Protein , 7 types, 30 molecules C1E1a1f1g1I1K1k1m1P1Q1R1r1s1t1S1T1V1W1X1Y1v1w1x1y1u1z1U1e1A

#1: Protein Baseplate hub protein, gp26


Mass: 49701.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS1
#2: Protein
Tail-tube, gp21


Mass: 14673.427 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHE7
#5: Protein
Tail sheath protein, gp20


Mass: 53896.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS8
#7: Protein
Tail Spike protein, gp124


Mass: 61649.805 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MGV0
#8: Protein
Short Tail Fibers, gp31


Mass: 31667.646 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHF3
#9: Protein Baseplate Centerpiece, gp25 / DNA-circularization protein


Mass: 43287.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFQ9
#10: Protein Baseplate Central Spike, gp27


Mass: 20720.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFZ0

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Baseplate Wedge ... , 3 types, 8 molecules F1G1h1i1H1j1J1l1

#3: Protein
Baseplate Wedge 2 protein, gp29


Mass: 43322.723 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFU4
#4: Protein Baseplate wedge 1, gp28


Mass: 19318.713 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus)
#6: Protein Baseplate Wedge 3 protein, gp30


Mass: 31414.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFT7

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Non-polymers , 1 types, 1 molecules

#11: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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-#10 / 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: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14856 / Symmetry type: POINT

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