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- PDB-9tic: Phage 812 baseplate in the pre-contraction state (C3) -

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Basic information

Entry
Database: PDB / ID: 9tic
TitlePhage 812 baseplate in the pre-contraction state (C3)
Components
  • CBM-cenC domain-containing protein
  • ORF49
  • ORF50
  • ORF56
  • ORF57
  • ORF58
  • ORF59
  • ORF60
  • ORF61
  • ORF62
  • ORF63
  • ORF64
  • ORF65
  • ORF67
  • ORF68
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / hydrolase activity, acting on glycosyl bonds / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process / proteolysis
Similarity search - Function
Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / : / Phi812 tail tube protein / : / ORF68-like, C-terminal domain ...Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Putative phage tail tube initiator protein / : / Lid domain of Phi812 weld protein / : / Phi812 tail tube protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / 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 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / LysM domain superfamily / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF60 / ORF59 ...CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF60 / ORF59 / ORF58 / ORF57 / ORF56 / ORF50 / ORF49
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsBinovsky, J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: EMBO J / Year: 2026
Title: Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.
Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos ...Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos Tripsianes / Pavel Plevka /
Abstract: Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of ...Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
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Revision 1.1Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: ORF68
1: ORF64
2: ORF65
3: ORF65
4: ORF65
5: ORF65
6: ORF65
7: ORF65
8: ORF68
9: ORF68
A: ORF58
AA: CBM-cenC domain-containing protein
AB: CBM-cenC domain-containing protein
AC: ORF50
AD: ORF50
AE: ORF50
AF: ORF50
AG: ORF50
AH: ORF50
AI: ORF49
AJ: ORF49
AK: ORF49
AL: ORF49
AM: ORF49
AN: ORF49
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: ORF64
Q: ORF64
R: ORF64
S: ORF64
T: ORF64
U: ORF64
V: ORF64
W: ORF64
X: ORF64
Y: ORF64
Z: ORF64
a: CBM-cenC domain-containing protein
b: CBM-cenC domain-containing protein
c: CBM-cenC domain-containing protein
d: ORF67
e: ORF64
f: ORF64
g: ORF64
h: ORF64
i: ORF64
j: ORF64
k: ORF64
l: ORF64
m: ORF64
n: ORF64
o: ORF64
p: ORF64
q: ORF65
r: ORF65
s: ORF65
t: ORF65
u: ORF65
v: ORF65
w: ORF68
x: ORF68
y: ORF68
z: CBM-cenC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)4,013,76876
Polymers4,013,76876
Non-polymers00
Water00
1
0: ORF68
1: ORF64
2: ORF65
3: ORF65
4: ORF65
5: ORF65
6: ORF65
7: ORF65
8: ORF68
9: ORF68
A: ORF58
AA: CBM-cenC domain-containing protein
AB: CBM-cenC domain-containing protein
AC: ORF50
AD: ORF50
AE: ORF50
AF: ORF50
AG: ORF50
AH: ORF50
AI: ORF49
AJ: ORF49
AK: ORF49
AL: ORF49
AM: ORF49
AN: ORF49
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: ORF64
Q: ORF64
R: ORF64
S: ORF64
T: ORF64
U: ORF64
V: ORF64
W: ORF64
X: ORF64
Y: ORF64
Z: ORF64
a: CBM-cenC domain-containing protein
b: CBM-cenC domain-containing protein
c: CBM-cenC domain-containing protein
d: ORF67
e: ORF64
f: ORF64
g: ORF64
h: ORF64
i: ORF64
j: ORF64
k: ORF64
l: ORF64
m: ORF64
n: ORF64
o: ORF64
p: ORF64
q: ORF65
r: ORF65
s: ORF65
t: ORF65
u: ORF65
v: ORF65
w: ORF68
x: ORF68
y: ORF68
z: CBM-cenC domain-containing protein

0: ORF68
1: ORF64
2: ORF65
3: ORF65
4: ORF65
5: ORF65
6: ORF65
7: ORF65
8: ORF68
9: ORF68
A: ORF58
AA: CBM-cenC domain-containing protein
AB: CBM-cenC domain-containing protein
AC: ORF50
AD: ORF50
AE: ORF50
AF: ORF50
AG: ORF50
AH: ORF50
AI: ORF49
AJ: ORF49
AK: ORF49
AL: ORF49
AM: ORF49
AN: ORF49
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: ORF64
Q: ORF64
R: ORF64
S: ORF64
T: ORF64
U: ORF64
V: ORF64
W: ORF64
X: ORF64
Y: ORF64
Z: ORF64
a: CBM-cenC domain-containing protein
b: CBM-cenC domain-containing protein
c: CBM-cenC domain-containing protein
d: ORF67
e: ORF64
f: ORF64
g: ORF64
h: ORF64
i: ORF64
j: ORF64
k: ORF64
l: ORF64
m: ORF64
n: ORF64
o: ORF64
p: ORF64
q: ORF65
r: ORF65
s: ORF65
t: ORF65
u: ORF65
v: ORF65
w: ORF68
x: ORF68
y: ORF68
z: CBM-cenC domain-containing protein

0: ORF68
1: ORF64
2: ORF65
3: ORF65
4: ORF65
5: ORF65
6: ORF65
7: ORF65
8: ORF68
9: ORF68
A: ORF58
AA: CBM-cenC domain-containing protein
AB: CBM-cenC domain-containing protein
AC: ORF50
AD: ORF50
AE: ORF50
AF: ORF50
AG: ORF50
AH: ORF50
AI: ORF49
AJ: ORF49
AK: ORF49
AL: ORF49
AM: ORF49
AN: ORF49
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: ORF64
Q: ORF64
R: ORF64
S: ORF64
T: ORF64
U: ORF64
V: ORF64
W: ORF64
X: ORF64
Y: ORF64
Z: ORF64
a: CBM-cenC domain-containing protein
b: CBM-cenC domain-containing protein
c: CBM-cenC domain-containing protein
d: ORF67
e: ORF64
f: ORF64
g: ORF64
h: ORF64
i: ORF64
j: ORF64
k: ORF64
l: ORF64
m: ORF64
n: ORF64
o: ORF64
p: ORF64
q: ORF65
r: ORF65
s: ORF65
t: ORF65
u: ORF65
v: ORF65
w: ORF68
x: ORF68
y: ORF68
z: CBM-cenC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)12,041,303228
Polymers12,041,303228
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

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Protein , 15 types, 76 molecules 089wxy1PQRSTUVWXYZefghijklmnop...

#1: Protein
ORF68 / Putative receptor binding protein


Mass: 50474.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7P9
#2: Protein ...
ORF64


Mass: 19259.613 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q3
#3: Protein
ORF65


Mass: 129262.961 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q2
#4: 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
#5: Protein
CBM-cenC domain-containing protein


Mass: 72654.742 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A0A0U1UXW5
#6: Protein
ORF50 / Putative tail tube protein


Mass: 15942.970 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R7
#7: Protein
ORF49 / Putative tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R8
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: Protein ORF67 / Putative DUF2977 domain protein


Mass: 14627.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q0

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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: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3586 / Symmetry type: POINT
Atomic model buildingB value: 287 / Protocol: RIGID BODY FIT / Space: REAL
Details: Fitting of previously refined sub-models (e.g. lower arm, upper arm, core, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body ...Details: Fitting of previously refined sub-models (e.g. lower arm, upper arm, core, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (all chains as a single rigid body).

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