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- PDB-5iv7: Cryo-electron microscopy structure of the star-shaped, hubless po... -

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Basic information

Entry
Database: PDB / ID: 5iv7
TitleCryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate
Components(Baseplate wedge protein ...) x 8
KeywordsVIRAL PROTEIN / T4 / baseplate / post-attachment / bacteriophage / bacterial virus / star-shaped / hubless / membrane-piercing / cell attachment / infection
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding
Similarity search - Function
Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate structural protein Gp11 ...Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Baseplate wedge protein gp53 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.77 Å
AuthorsTaylor, N.M.I. / Guerrero-Ferreira, R.C. / Goldie, K.N. / Stahlberg, H. / Leiman, P.G.
CitationJournal: Nature / Year: 2016
Title: Structure of the T4 baseplate and its function in triggering sheath contraction.
Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /
Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
History
DepositionMar 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.details / _em_software.name
Revision 1.4Feb 7, 2018Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.energyfilter_lower

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Baseplate wedge protein gp6
B: Baseplate wedge protein gp6
C: Baseplate wedge protein gp7
D: Baseplate wedge protein gp8
E: Baseplate wedge protein gp8
F: Baseplate wedge protein gp9
G: Baseplate wedge protein gp9
H: Baseplate wedge protein gp9
I: Baseplate wedge protein gp10
J: Baseplate wedge protein gp10
K: Baseplate wedge protein gp10
L: Baseplate wedge protein gp11
M: Baseplate wedge protein gp11
N: Baseplate wedge protein gp11
O: Baseplate wedge protein gp25
P: Baseplate wedge protein gp53
Q: Baseplate wedge protein gp6
R: Baseplate wedge protein gp6
S: Baseplate wedge protein gp7
T: Baseplate wedge protein gp8
U: Baseplate wedge protein gp8
V: Baseplate wedge protein gp9
W: Baseplate wedge protein gp9
X: Baseplate wedge protein gp9
Y: Baseplate wedge protein gp10
Z: Baseplate wedge protein gp10
a: Baseplate wedge protein gp10
b: Baseplate wedge protein gp11
c: Baseplate wedge protein gp11
d: Baseplate wedge protein gp11
e: Baseplate wedge protein gp25
f: Baseplate wedge protein gp53
g: Baseplate wedge protein gp6
h: Baseplate wedge protein gp6
i: Baseplate wedge protein gp7
j: Baseplate wedge protein gp8
k: Baseplate wedge protein gp8
l: Baseplate wedge protein gp9
m: Baseplate wedge protein gp9
n: Baseplate wedge protein gp9
o: Baseplate wedge protein gp10
p: Baseplate wedge protein gp10
q: Baseplate wedge protein gp10
r: Baseplate wedge protein gp11
s: Baseplate wedge protein gp11
t: Baseplate wedge protein gp11
u: Baseplate wedge protein gp25
v: Baseplate wedge protein gp53
w: Baseplate wedge protein gp6
x: Baseplate wedge protein gp6
y: Baseplate wedge protein gp7
z: Baseplate wedge protein gp8
AA: Baseplate wedge protein gp8
AB: Baseplate wedge protein gp9
AC: Baseplate wedge protein gp9
AD: Baseplate wedge protein gp9
AE: Baseplate wedge protein gp10
AF: Baseplate wedge protein gp10
AG: Baseplate wedge protein gp10
BA: Baseplate wedge protein gp11
BB: Baseplate wedge protein gp11
BC: Baseplate wedge protein gp11
BD: Baseplate wedge protein gp25
BE: Baseplate wedge protein gp53
BF: Baseplate wedge protein gp6
BG: Baseplate wedge protein gp6
CA: Baseplate wedge protein gp7
CB: Baseplate wedge protein gp8
CC: Baseplate wedge protein gp8
CD: Baseplate wedge protein gp9
CE: Baseplate wedge protein gp9
CF: Baseplate wedge protein gp9
CG: Baseplate wedge protein gp10
DA: Baseplate wedge protein gp10
DB: Baseplate wedge protein gp10
DC: Baseplate wedge protein gp11
DD: Baseplate wedge protein gp11
DE: Baseplate wedge protein gp11
DF: Baseplate wedge protein gp25
DG: Baseplate wedge protein gp53
EA: Baseplate wedge protein gp6
EB: Baseplate wedge protein gp6
EC: Baseplate wedge protein gp7
ED: Baseplate wedge protein gp8
EE: Baseplate wedge protein gp8
EF: Baseplate wedge protein gp9
EG: Baseplate wedge protein gp9
FA: Baseplate wedge protein gp9
FB: Baseplate wedge protein gp10
FC: Baseplate wedge protein gp10
FD: Baseplate wedge protein gp10
FE: Baseplate wedge protein gp11
FF: Baseplate wedge protein gp11
FG: Baseplate wedge protein gp11
GA: Baseplate wedge protein gp25
GB: Baseplate wedge protein gp53


Theoretical massNumber of molelcules
Total (without water)4,473,61796
Polymers4,473,61796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area828600 Å2
ΔGint-4444 kcal/mol
Surface area1538310 Å2
MethodPISA

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Components

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Baseplate wedge protein ... , 8 types, 96 molecules ABQRghwxBFBGEAEBCSiyCAECDETUjkzAACBCCEDEE...

#1: Protein
Baseplate wedge protein gp6 / Gene product 6 / gp6


Mass: 74492.641 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P19060
#2: Protein
Baseplate wedge protein gp7 / Gene product 7 / gp7


Mass: 119336.516 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P19061
#3: Protein
Baseplate wedge protein gp8 / Gene product 8 / gp8


Mass: 38041.668 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P19062
#4: Protein
Baseplate wedge protein gp9 / Gene product 9 / gp9


Mass: 31024.725 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10927
#5: Protein
Baseplate wedge protein gp10 / Gene product 10 / gp10


Mass: 66281.680 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10928
#6: Protein
Baseplate wedge protein gp11 / Gene product 11 / gp11


Mass: 23725.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10929
#7: Protein
Baseplate wedge protein gp25 / Outer wedge of baseplate protein / Protein Gp25


Mass: 15111.101 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P09425
#8: Protein
Baseplate wedge protein gp53 / Gene product 53 / gp53


Mass: 22990.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P16011

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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: Star-shaped, hubless post-attachment T4 baseplate-tail tube complex
Type: COMPLEX
Details: The short tail fibers (gp12 trimers) appear more flexible, and no special effort was made to reconstruct them. They were partly masked out by the circular mask.The total mass of the ...Details: The short tail fibers (gp12 trimers) appear more flexible, and no special effort was made to reconstruct them. They were partly masked out by the circular mask.The total mass of the reconstructed volume was approximately 4.5 MDa (excluding short tail fibers). The short-tail fibers were not included in the PDB file.
Entity ID: all / Source: NATURAL
Molecular weightValue: 5.5 MDa / Experimental value: NO
Source (natural)Organism: Enterobacteria phage T4 (virus) / Strain: am18/am23 mutant
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRIS-hydrochloride pH 8TRIS-HCl1
2100 mMsodium chlorideNaCl1
38 mMmagnesium sulfateMgSO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current model is that star-shaped, ...Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current model is that star-shaped, hubless post-attachment baseplate.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Applied 3.5 ul of sample and blotting 3 seconds before plunging

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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 FIELD / Nominal magnification: 105000 X / Calibrated magnification: 37700 X / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: HELIUM / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 40 / Used frames/image: 3-40

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
4CTFFIND4CTF correction
5RELION1.4CTF correction
8Coot0.8.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
14PHENIX1.10.1-2155model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 47516
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 6.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5176 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 5IV5

5iv5

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