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- PDB-9eug: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 b... -

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Basic information

Entry
Database: PDB / ID: 9eug
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - core, wedge module, and proximal tail proteins
Components
  • (Baseplate component) x 2
  • Baseplate wedge subunit
  • Capsid protein
  • GP-PDE domain-containing protein
  • Major tail sheath protein
  • NlpC/P60 domain-containing protein
  • Peptidase C51 domain-containing protein
  • Putative baseplate component
  • TmpF
KeywordsVIRUS / bacteriophage / phage / contractile / phi812 / baseplate
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process
Similarity search - Function
Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Baseplate protein J-like ...Putative phage tail tube initiator protein / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / CHAP domain profile. / CHAP domain / CHAP domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Baseplate protein J-like / Baseplate J-like protein / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / LysM domain superfamily / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Baseplate component / Baseplate wedge subunit / NlpC/P60 domain-containing protein / Baseplate component / GP-PDE domain-containing protein / TmpF / Major tail sheath protein / Peptidase C51 domain-containing protein / Putative baseplate component / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBinovsky, J. / Siborova, M. / Baska, R. / Pichel-Beleiro, A. / Skubnik, K. / Novacek, J. / van Raaij, M.J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Siborova, M. / Baska, R. / Pichel-Beleiro, A. / Skubnik, K. / Novacek, J. / van Raaij, M.J. / Plevka, P.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein


Theoretical massNumber of molelcules
Total (without water)1,246,98127
Polymers1,246,98127
Non-polymers00
Water00
1
A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein

A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein

A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein

A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein

A: NlpC/P60 domain-containing protein
B: GP-PDE domain-containing protein
C: Baseplate component
D: Baseplate component
E: Peptidase C51 domain-containing protein
F: Baseplate component
G: Baseplate component
H: TmpF
I: Baseplate component
J: TmpF
K: Baseplate component
L: Baseplate wedge subunit
M: Putative baseplate component
N: Putative baseplate component
O: Baseplate wedge subunit
P: Major tail sheath protein
Q: Major tail sheath protein
R: Capsid protein
S: Capsid protein
T: Major tail sheath protein
U: Major tail sheath protein
V: Capsid protein
W: Capsid protein
X: Major tail sheath protein
Y: Major tail sheath protein
Z: Capsid protein
a: Capsid protein


Theoretical massNumber of molelcules
Total (without water)6,234,906135
Polymers6,234,906135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
MethodUCSF CHIMERA

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Components

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Protein , 10 types, 27 molecules ABCDIKEFGHJLOMNPQTUXYRSVWZa

#1: Protein NlpC/P60 domain-containing protein / weld protein


Mass: 34645.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1UXW0
#2: Protein GP-PDE domain-containing protein / central spike protein


Mass: 96199.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WFD7
#3: Protein
Baseplate component / wedge protein


Mass: 39248.859 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WF63
#4: Protein Peptidase C51 domain-containing protein / hub protein


Mass: 91364.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1X189
#5: Protein Baseplate component / assembly protein


Mass: 19998.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1UXD6
#6: Protein TmpF / arm scaffold protein


Mass: 116389.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WGD3
#7: Protein Baseplate wedge subunit / sheath initiator protein


Mass: 26611.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1UXD7
#8: Protein Putative baseplate component / tube initiator protein


Mass: 29381.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1X2L4
#9: Protein
Major tail sheath protein / tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WZ79
#10: Protein
Capsid protein / tail tube protein


Mass: 15942.970 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A1YTP2

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Details

Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus phage 812VIRUS#4, #6-#7, #5, #8, #3, #2, #1, #10, #90NATURAL
2TailCOMPLEX#4, #6-#7, #5, #8, #3, #2, #1, #10, #91NATURAL
3Tail tubeCOMPLEX#102NATURAL
4Tail sheathCOMPLEX#92NATURAL
5BaseplateCOMPLEX#4, #6-#7, #5, #8, #3, #2, #12NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage 812 (virus)307898
32Staphylococcus phage 812 (virus)307898
43Staphylococcus phage 812 (virus)307898
54Staphylococcus phage 812 (virus)307898
65Staphylococcus phage 812 (virus)307898
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 8 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 1 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 18

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 23421
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9705 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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