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- PDB-9k3m: The structure of Microviridae PJNS001 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9k3m
TitleThe structure of Microviridae PJNS001
Components
  • Capsid protein F
  • DNA-binding protein J
  • Major spike protein G
KeywordsVIRUS / structual proteins
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Viral coat protein subunit
Similarity search - Domain/homology
Major spike protein G / DNA-binding protein J / Capsid protein F
Similarity search - Component
Biological speciesMicroviridae (isometric ssDNA phages)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsHu, W.L. / Chen, Y.B. / Wei, Y.M. / Gao, Y.
Funding support1items
OrganizationGrant numberCountry
Other government23QA1406400
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis for Salmonella infection by two Microviridae phages.
Authors: Wanlong Hu / Zhengjie Liu / Yuming Wei / Qucheng Bian / Weiqi Lan / Chongzheng Fan / Jiaoyang Song / Qianqian Sun / Xiaojie Zhang / Yuqing Liu / Yan Gao / Yibao Chen /
Abstract: The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage ...The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage therapy. Microviridae phages offer a promising model for studying phage-host interactions with their unique structural and infection mechanisms. Here, we identify two Microviridae phages, PJNS001 and PJNS002, with different host receptor dependencies, and determine their cryo-EM structures at 2.68 Å and 2.59 Å resolution, respectively. These icosahedral capsids with T = 1 symmetry exhibit a unique vertex reinforcement mechanism, stabilizing the viral assembly. The specific pentameric adaptations, coupled with DNA binding protein engagements and thermodynamic constraints, collectively preclude the formation of hybrid virions. Structural analysis and in situ visualization reveal spike protein features and host-attachment intermediates, informing host specificity. Together, these findings advance our understanding of Microviridae infection mechanisms and provide a structural framework for rational phage design against antibiotic-resistant pathogens.
History
DepositionOct 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Capsid protein F
G: Major spike protein G
J: DNA-binding protein J
A: Capsid protein F
B: Major spike protein G
C: DNA-binding protein J
D: Capsid protein F
E: Major spike protein G
H: DNA-binding protein J
I: Capsid protein F
K: Major spike protein G
L: DNA-binding protein J
M: Capsid protein F
N: Major spike protein G
O: DNA-binding protein J
P: Capsid protein F
Q: Major spike protein G
R: DNA-binding protein J
S: Capsid protein F
T: Major spike protein G
V: DNA-binding protein J
W: Capsid protein F
X: Major spike protein G
Y: DNA-binding protein J
Z: Capsid protein F
AA: Major spike protein G
BA: DNA-binding protein J
CA: Capsid protein F
DA: Major spike protein G
EA: DNA-binding protein J
FA: Capsid protein F
GA: Major spike protein G
HA: DNA-binding protein J
IA: Capsid protein F
JA: Major spike protein G
KA: DNA-binding protein J
LA: Capsid protein F
MA: Major spike protein G
NA: DNA-binding protein J
OA: Capsid protein F
PA: Major spike protein G
QA: DNA-binding protein J
RA: Capsid protein F
SA: Major spike protein G
TA: DNA-binding protein J
UA: Capsid protein F
VA: Major spike protein G
WA: DNA-binding protein J
XA: Capsid protein F
YA: Major spike protein G
ZA: DNA-binding protein J
AB: Capsid protein F
BB: Major spike protein G
CB: DNA-binding protein J
DB: Capsid protein F
EB: Major spike protein G
FB: DNA-binding protein J
GB: Capsid protein F
HB: Major spike protein G
IB: DNA-binding protein J
JB: Capsid protein F
KB: Major spike protein G
LB: DNA-binding protein J
MB: Capsid protein F
NB: Major spike protein G
OB: DNA-binding protein J
PB: Capsid protein F
QB: Major spike protein G
RB: DNA-binding protein J
SB: Capsid protein F
TB: Major spike protein G
UB: DNA-binding protein J
VB: Capsid protein F
WB: Major spike protein G
XB: DNA-binding protein J
YB: Capsid protein F
ZB: Major spike protein G
AC: DNA-binding protein J
BC: Capsid protein F
CC: Major spike protein G
DC: DNA-binding protein J
EC: Capsid protein F
FC: Major spike protein G
GC: DNA-binding protein J
HC: Capsid protein F
IC: Major spike protein G
JC: DNA-binding protein J
KC: Capsid protein F
LC: Major spike protein G
MC: DNA-binding protein J
NC: Capsid protein F
OC: Major spike protein G
PC: DNA-binding protein J
QC: Capsid protein F
RC: Major spike protein G
SC: DNA-binding protein J
TC: Capsid protein F
UC: Major spike protein G
VC: DNA-binding protein J
WC: Capsid protein F
XC: Major spike protein G
YC: DNA-binding protein J
ZC: Capsid protein F
AD: Major spike protein G
BD: DNA-binding protein J
CD: Capsid protein F
DD: Major spike protein G
ED: DNA-binding protein J
FD: Capsid protein F
GD: Major spike protein G
HD: DNA-binding protein J
ID: Capsid protein F
JD: Major spike protein G
KD: DNA-binding protein J
LD: Capsid protein F
MD: Major spike protein G
ND: DNA-binding protein J
OD: Capsid protein F
PD: Major spike protein G
QD: DNA-binding protein J
RD: Capsid protein F
SD: Major spike protein G
TD: DNA-binding protein J
UD: Capsid protein F
VD: Major spike protein G
WD: DNA-binding protein J
XD: Capsid protein F
YD: Major spike protein G
ZD: DNA-binding protein J
AE: Capsid protein F
BE: Major spike protein G
CE: DNA-binding protein J
DE: Capsid protein F
EE: Major spike protein G
FE: DNA-binding protein J
GE: Capsid protein F
HE: Major spike protein G
IE: DNA-binding protein J
JE: Capsid protein F
KE: Major spike protein G
LE: DNA-binding protein J
ME: Capsid protein F
NE: Major spike protein G
OE: DNA-binding protein J
PE: Capsid protein F
QE: Major spike protein G
RE: DNA-binding protein J
SE: Capsid protein F
TE: Major spike protein G
UE: DNA-binding protein J
VE: Capsid protein F
WE: Major spike protein G
XE: DNA-binding protein J
YE: Capsid protein F
ZE: Major spike protein G
AF: DNA-binding protein J
BF: Capsid protein F
CF: Major spike protein G
DF: DNA-binding protein J
EF: Capsid protein F
FF: Major spike protein G
GF: DNA-binding protein J
HF: Capsid protein F
IF: Major spike protein G
JF: DNA-binding protein J
KF: Capsid protein F
LF: Major spike protein G
MF: DNA-binding protein J
NF: Capsid protein F
OF: Major spike protein G
PF: DNA-binding protein J
QF: Capsid protein F
RF: Major spike protein G
SF: DNA-binding protein J
TF: Capsid protein F
UF: Major spike protein G
VF: DNA-binding protein J
WF: Capsid protein F
XF: Major spike protein G
YF: DNA-binding protein J


Theoretical massNumber of molelcules
Total (without water)4,311,132180
Polymers4,311,132180
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein F / F protein / GPF


Mass: 48500.480 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Microviridae (isometric ssDNA phages) / Strain: PJNS001 / References: UniProt: Q2LLZ1
#2: Protein ...
Major spike protein G / G protein / GPG


Mass: 19112.695 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Microviridae (isometric ssDNA phages) / Strain: PJNS001 / References: UniProt: A0A5J6T840
#3: Protein/peptide ...
DNA-binding protein J / J protein / Small core protein


Mass: 4239.017 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Microviridae (isometric ssDNA phages) / Strain: PJNS001 / References: UniProt: P69592
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: Microviridae / Type: VIRUS / Details: T=1 icosahedral virus / Entity ID: all / Source: NATURAL
Molecular weightValue: 4.31 MDa / Experimental value: NO
Source (natural)Organism: Microviridae (isometric ssDNA phages) / Strain: PJNS001
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Salmonella
Virus shellDiameter: 290 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.5 / Details: pH 7.2~7.6
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mmol/Lsodium chlorideNaCl1
22.65 mmol/Lpotassium chlorideKCl1
310 mmol/Ldibasic sodium phosphateNa2HPO41
41.75 mmol/Lpotassium dihydrogen phosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.25 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4808
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.0.1particle selection
2SerialEM4.1.9image acquisition
4cryoSPARC4.0.1CTF correction
7PHENIX1.20.1model fitting
9cryoSPARC4.0.1initial Euler assignment
10cryoSPARC4.0.1final Euler assignment
11cryoSPARC4.0.1classification
12cryoSPARC4.0.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 711275
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16905 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 15.89 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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