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- PDB-9tid: Phage 812 baseplate in the pre-contraction state - core and wedge... -

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Basic information

Entry
Database: PDB / ID: 9tid
TitlePhage 812 baseplate in the pre-contraction state - core and wedge module proteins
Components
  • ORF49
  • ORF56
  • ORF57
  • ORF58
  • ORF59
  • ORF60
  • ORF61
  • ORF62
  • ORF63
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process / proteolysis
Similarity search - Function
: / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family ...: / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain / Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / CHAP domain profile. / CHAP domain / CHAP domain / 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
ORF63 / ORF62 / ORF61 / ORF60 / ORF59 / ORF58 / ORF57 / ORF56 / ORF49
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBinovsky, 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: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812
Authors: Binovsky, J. / Plevka, P.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF58
B: ORF57
C: ORF56
D: ORF60
E: ORF60
F: ORF59
G: ORF59
H: ORF61
I: ORF61
J: ORF62
K: ORF62
L: ORF62
M: ORF62
N: ORF63
O: ORF63
P: ORF49
Q: ORF49
R: ORF49
S: ORF49


Theoretical massNumber of molelcules
Total (without water)1,022,20519
Polymers1,022,20519
Non-polymers00
Water00
1
A: ORF58
B: ORF57
C: ORF56
D: ORF60
E: ORF60
F: ORF59
G: ORF59
H: ORF61
I: ORF61
J: ORF62
K: ORF62
L: ORF62
M: ORF62
N: ORF63
O: ORF63
P: ORF49
Q: ORF49
R: ORF49
S: ORF49

A: ORF58
B: ORF57
C: ORF56
D: ORF60
E: ORF60
F: ORF59
G: ORF59
H: ORF61
I: ORF61
J: ORF62
K: ORF62
L: ORF62
M: ORF62
N: ORF63
O: ORF63
P: ORF49
Q: ORF49
R: ORF49
S: ORF49

A: ORF58
B: ORF57
C: ORF56
D: ORF60
E: ORF60
F: ORF59
G: ORF59
H: ORF61
I: ORF61
J: ORF62
K: ORF62
L: ORF62
M: ORF62
N: ORF63
O: ORF63
P: ORF49
Q: ORF49
R: ORF49
S: ORF49


Theoretical massNumber of molelcules
Total (without water)3,066,61657
Polymers3,066,61657
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

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Protein , 9 types, 19 molecules ABCDEFGHIJKLMNOPQRS

#1: Protein ORF58 / Putative phosphodiesterase


Mass: 96199.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q9
#2: Protein ORF57 / Putative cysteine protease


Mass: 34645.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R0
#3: Protein ORF56 / Putative CHAP domain protein


Mass: 91364.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R1
#4: Protein ORF60


Mass: 19998.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q7
#5: Protein ORF59


Mass: 29381.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q8
#6: Protein ORF61


Mass: 26611.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q6
#7: Protein
ORF62 / Putative baseplate protein


Mass: 39248.859 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q5
#8: Protein ORF63


Mass: 116389.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q4
#9: Protein
ORF49 / Putative tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R8

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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

ComponentName: Staphylococcus phage 812K1/420 / Type: VIRUS
Details: Propagated in S. aureus SA 812 (CCM 4028) planktonic culture and purified on a CsCl gradient.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisTris1
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10e9 PFU/ml
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 26731

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
4GctfCTF correction
7UCSF ChimeraX1.9model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 64874
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8368 / Symmetry type: POINT
Atomic model buildingB value: 35.8 / Protocol: FLEXIBLE FIT / Space: REAL

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