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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: To Be Published
Title: Structural and Functional Insights into Microviridae PJNS001 and PJNS002 target Salmonella
Authors: Hu, W.L. / Gao, Y.
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
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 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
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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