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- PDB-9lw6: Top cap of bacteriophage Mycofy1 mature head (C5 symmetry) -

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Basic information

Entry
Database: PDB / ID: 9lw6
TitleTop cap of bacteriophage Mycofy1 mature head (C5 symmetry)
ComponentsPhage capsid-like C-terminal domain-containing protein
KeywordsVIRAL PROTEIN / Mycobacterium / bacteriophage / prolate head / major capsid protein / VIRUS
Function / homology: / Phage capsid / Phage capsid family / virion component / Phage capsid-like C-terminal domain-containing protein
Function and homology information
Biological speciesMycolicibacterium phage Mycofy1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLi, X. / Shao, Q. / Li, L. / Xie, L. / Ruan, Z. / Fang, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Shenzhen Science and Technology ProgramJCYJ20240813180500001 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM reveals structural diversity in prolate-headed mycobacteriophage Mycofy1.
Authors: Xiangyun Li / Qianqian Shao / Lin Li / Linlin Xie / Zhiyang Ruan / Qianglin Fang /
Abstract: Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that ...Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that Mycofy1 possesses a prolate head and a long non-contractile tail. We determined structures of its head, head-to-tail interface, terminator, and tail tube to resolutions of ∼3.5 Å. Unexpectedly, we identified two distinct types of prolate head structures, exhibiting a 36-degree relative rotation in the top cap region. Additionally, the head-to-tail interface demonstrated flexibility. Our structures provide the first high-resolution cryo-EM data of a mycobacteriophage with a prolate head, as well as detailed structural information of the head-to-tail interface and head-proximal tail region in this phage group. These findings advance our understanding of assembly mechanisms in tailed bacteriophages.
History
DepositionFeb 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage capsid-like C-terminal domain-containing protein
B: Phage capsid-like C-terminal domain-containing protein
C: Phage capsid-like C-terminal domain-containing protein
D: Phage capsid-like C-terminal domain-containing protein
E: Phage capsid-like C-terminal domain-containing protein
F: Phage capsid-like C-terminal domain-containing protein
G: Phage capsid-like C-terminal domain-containing protein
H: Phage capsid-like C-terminal domain-containing protein
I: Phage capsid-like C-terminal domain-containing protein
J: Phage capsid-like C-terminal domain-containing protein
K: Phage capsid-like C-terminal domain-containing protein
L: Phage capsid-like C-terminal domain-containing protein
M: Phage capsid-like C-terminal domain-containing protein
N: Phage capsid-like C-terminal domain-containing protein
O: Phage capsid-like C-terminal domain-containing protein
P: Phage capsid-like C-terminal domain-containing protein
Q: Phage capsid-like C-terminal domain-containing protein
R: Phage capsid-like C-terminal domain-containing protein
S: Phage capsid-like C-terminal domain-containing protein
T: Phage capsid-like C-terminal domain-containing protein
U: Phage capsid-like C-terminal domain-containing protein
V: Phage capsid-like C-terminal domain-containing protein
W: Phage capsid-like C-terminal domain-containing protein
X: Phage capsid-like C-terminal domain-containing protein
Y: Phage capsid-like C-terminal domain-containing protein
Z: Phage capsid-like C-terminal domain-containing protein
a: Phage capsid-like C-terminal domain-containing protein
b: Phage capsid-like C-terminal domain-containing protein
c: Phage capsid-like C-terminal domain-containing protein
d: Phage capsid-like C-terminal domain-containing protein
e: Phage capsid-like C-terminal domain-containing protein
f: Phage capsid-like C-terminal domain-containing protein
g: Phage capsid-like C-terminal domain-containing protein
h: Phage capsid-like C-terminal domain-containing protein
i: Phage capsid-like C-terminal domain-containing protein
j: Phage capsid-like C-terminal domain-containing protein
k: Phage capsid-like C-terminal domain-containing protein
l: Phage capsid-like C-terminal domain-containing protein
m: Phage capsid-like C-terminal domain-containing protein
n: Phage capsid-like C-terminal domain-containing protein
o: Phage capsid-like C-terminal domain-containing protein
p: Phage capsid-like C-terminal domain-containing protein
q: Phage capsid-like C-terminal domain-containing protein
r: Phage capsid-like C-terminal domain-containing protein
s: Phage capsid-like C-terminal domain-containing protein
t: Phage capsid-like C-terminal domain-containing protein
u: Phage capsid-like C-terminal domain-containing protein
v: Phage capsid-like C-terminal domain-containing protein
w: Phage capsid-like C-terminal domain-containing protein
1: Phage capsid-like C-terminal domain-containing protein
2: Phage capsid-like C-terminal domain-containing protein
3: Phage capsid-like C-terminal domain-containing protein
4: Phage capsid-like C-terminal domain-containing protein
5: Phage capsid-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)3,227,97254
Polymers3,227,97254
Non-polymers00
Water00
1
A: Phage capsid-like C-terminal domain-containing protein
B: Phage capsid-like C-terminal domain-containing protein
C: Phage capsid-like C-terminal domain-containing protein
D: Phage capsid-like C-terminal domain-containing protein
E: Phage capsid-like C-terminal domain-containing protein
F: Phage capsid-like C-terminal domain-containing protein
G: Phage capsid-like C-terminal domain-containing protein
H: Phage capsid-like C-terminal domain-containing protein
I: Phage capsid-like C-terminal domain-containing protein
J: Phage capsid-like C-terminal domain-containing protein
K: Phage capsid-like C-terminal domain-containing protein
L: Phage capsid-like C-terminal domain-containing protein
M: Phage capsid-like C-terminal domain-containing protein
N: Phage capsid-like C-terminal domain-containing protein
O: Phage capsid-like C-terminal domain-containing protein
P: Phage capsid-like C-terminal domain-containing protein
Q: Phage capsid-like C-terminal domain-containing protein
R: Phage capsid-like C-terminal domain-containing protein
S: Phage capsid-like C-terminal domain-containing protein
T: Phage capsid-like C-terminal domain-containing protein
U: Phage capsid-like C-terminal domain-containing protein
V: Phage capsid-like C-terminal domain-containing protein
W: Phage capsid-like C-terminal domain-containing protein
X: Phage capsid-like C-terminal domain-containing protein
Y: Phage capsid-like C-terminal domain-containing protein
Z: Phage capsid-like C-terminal domain-containing protein
a: Phage capsid-like C-terminal domain-containing protein
b: Phage capsid-like C-terminal domain-containing protein
c: Phage capsid-like C-terminal domain-containing protein
d: Phage capsid-like C-terminal domain-containing protein
e: Phage capsid-like C-terminal domain-containing protein
f: Phage capsid-like C-terminal domain-containing protein
g: Phage capsid-like C-terminal domain-containing protein
h: Phage capsid-like C-terminal domain-containing protein
i: Phage capsid-like C-terminal domain-containing protein
j: Phage capsid-like C-terminal domain-containing protein
k: Phage capsid-like C-terminal domain-containing protein
l: Phage capsid-like C-terminal domain-containing protein
m: Phage capsid-like C-terminal domain-containing protein
n: Phage capsid-like C-terminal domain-containing protein
o: Phage capsid-like C-terminal domain-containing protein
p: Phage capsid-like C-terminal domain-containing protein
q: Phage capsid-like C-terminal domain-containing protein
r: Phage capsid-like C-terminal domain-containing protein
s: Phage capsid-like C-terminal domain-containing protein
t: Phage capsid-like C-terminal domain-containing protein
u: Phage capsid-like C-terminal domain-containing protein
v: Phage capsid-like C-terminal domain-containing protein
w: Phage capsid-like C-terminal domain-containing protein
1: Phage capsid-like C-terminal domain-containing protein
2: Phage capsid-like C-terminal domain-containing protein
3: Phage capsid-like C-terminal domain-containing protein
4: Phage capsid-like C-terminal domain-containing protein
5: Phage capsid-like C-terminal domain-containing protein
x 5


Theoretical massNumber of molelcules
Total (without water)16,139,861270
Polymers16,139,861270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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: C5 (5 fold cyclic))

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Components

#1: Protein ...
Phage capsid-like C-terminal domain-containing protein / Major capsid protein gp6


Mass: 59777.262 Da / Num. of mol.: 54 / Source method: isolated from a natural source
Details: Sequence reference for Mycolicibacterium phage Mycofy1 is not available at the time of biocuration. Current sequence reference is from UniProt id Q854Z2.
Source: (natural) Mycolicibacterium phage Mycofy1 (virus) / References: UniProt: Q854Z2
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: Mycolicibacterium phage Mycofy1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium phage Mycofy1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.09 sec. / Electron dose: 25.7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
9RELION4initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22074 / Details: Manual picking
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19765 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004123564
ELECTRON MICROSCOPYf_angle_d0.508168678
ELECTRON MICROSCOPYf_dihedral_angle_d4.10416920
ELECTRON MICROSCOPYf_chiral_restr0.04218714
ELECTRON MICROSCOPYf_plane_restr0.00522464

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