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- PDB-9k3n: The structure of Salmonella phage PJNS002 -

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Basic information

Entry
Database: PDB / ID: 9k3n
TitleThe structure of Salmonella phage PJNS002
Components
  • DNA (5'-D(P*AP*AP*AP*A)-3')
  • DNA (5'-D(P*AP*AP*AP*AP*A)-3')
  • DNA-binding protein J
  • capsid protein F
  • spike protein G
KeywordsVIRUS / structual proteins
Function / homologyDNA
Function and homology information
Biological speciesSalmonella phage PJNS002 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsHu, W.L. / Chen, Y.B. / Wei, Y.M. / Gao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government23QA1406400 China
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

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Assembly

Deposited unit
F: capsid protein F
G: spike protein G
J: DNA-binding protein J
A: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
U: DNA (5'-D(P*AP*AP*AP*A)-3')
B: capsid protein F
C: spike protein G
D: DNA-binding protein J
E: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
a: DNA (5'-D(P*AP*AP*AP*A)-3')
H: capsid protein F
I: spike protein G
K: DNA-binding protein J
L: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
b: DNA (5'-D(P*AP*AP*AP*A)-3')
M: capsid protein F
N: spike protein G
O: DNA-binding protein J
P: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
c: DNA (5'-D(P*AP*AP*AP*A)-3')
Q: capsid protein F
R: spike protein G
S: DNA-binding protein J
T: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
d: DNA (5'-D(P*AP*AP*AP*A)-3')
V: capsid protein F
W: spike protein G
X: DNA-binding protein J
Y: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
e: DNA (5'-D(P*AP*AP*AP*A)-3')
Z: capsid protein F
AA: spike protein G
BA: DNA-binding protein J
CA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
f: DNA (5'-D(P*AP*AP*AP*A)-3')
DA: capsid protein F
EA: spike protein G
FA: DNA-binding protein J
GA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
g: DNA (5'-D(P*AP*AP*AP*A)-3')
HA: capsid protein F
IA: spike protein G
JA: DNA-binding protein J
KA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
h: DNA (5'-D(P*AP*AP*AP*A)-3')
LA: capsid protein F
MA: spike protein G
NA: DNA-binding protein J
OA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
i: DNA (5'-D(P*AP*AP*AP*A)-3')
PA: capsid protein F
QA: spike protein G
RA: DNA-binding protein J
SA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
j: DNA (5'-D(P*AP*AP*AP*A)-3')
TA: capsid protein F
UA: spike protein G
VA: DNA-binding protein J
WA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
k: DNA (5'-D(P*AP*AP*AP*A)-3')
XA: capsid protein F
YA: spike protein G
ZA: DNA-binding protein J
AB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
l: DNA (5'-D(P*AP*AP*AP*A)-3')
BB: capsid protein F
CB: spike protein G
DB: DNA-binding protein J
EB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
m: DNA (5'-D(P*AP*AP*AP*A)-3')
FB: capsid protein F
GB: spike protein G
HB: DNA-binding protein J
IB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
n: DNA (5'-D(P*AP*AP*AP*A)-3')
JB: capsid protein F
KB: spike protein G
LB: DNA-binding protein J
MB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
o: DNA (5'-D(P*AP*AP*AP*A)-3')
NB: capsid protein F
OB: spike protein G
PB: DNA-binding protein J
QB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
p: DNA (5'-D(P*AP*AP*AP*A)-3')
RB: capsid protein F
SB: spike protein G
TB: DNA-binding protein J
UB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
q: DNA (5'-D(P*AP*AP*AP*A)-3')
VB: capsid protein F
WB: spike protein G
XB: DNA-binding protein J
YB: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
r: DNA (5'-D(P*AP*AP*AP*A)-3')
ZB: capsid protein F
AC: spike protein G
BC: DNA-binding protein J
CC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
s: DNA (5'-D(P*AP*AP*AP*A)-3')
DC: capsid protein F
EC: spike protein G
FC: DNA-binding protein J
GC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
t: DNA (5'-D(P*AP*AP*AP*A)-3')
HC: capsid protein F
IC: spike protein G
JC: DNA-binding protein J
KC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
u: DNA (5'-D(P*AP*AP*AP*A)-3')
LC: capsid protein F
MC: spike protein G
NC: DNA-binding protein J
OC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
v: DNA (5'-D(P*AP*AP*AP*A)-3')
PC: capsid protein F
QC: spike protein G
RC: DNA-binding protein J
SC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
w: DNA (5'-D(P*AP*AP*AP*A)-3')
TC: capsid protein F
UC: spike protein G
VC: DNA-binding protein J
WC: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
x: DNA (5'-D(P*AP*AP*AP*A)-3')
XC: capsid protein F
YC: spike protein G
ZC: DNA-binding protein J
AD: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
y: DNA (5'-D(P*AP*AP*AP*A)-3')
BD: capsid protein F
CD: spike protein G
DD: DNA-binding protein J
ED: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
z: DNA (5'-D(P*AP*AP*AP*A)-3')
FD: capsid protein F
GD: spike protein G
HD: DNA-binding protein J
ID: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
0: DNA (5'-D(P*AP*AP*AP*A)-3')
JD: capsid protein F
KD: spike protein G
LD: DNA-binding protein J
MD: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
1: DNA (5'-D(P*AP*AP*AP*A)-3')
ND: capsid protein F
OD: spike protein G
PD: DNA-binding protein J
QD: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
2: DNA (5'-D(P*AP*AP*AP*A)-3')
RD: capsid protein F
SD: spike protein G
TD: DNA-binding protein J
UD: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
3: DNA (5'-D(P*AP*AP*AP*A)-3')
VD: capsid protein F
WD: spike protein G
XD: DNA-binding protein J
YD: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
4: DNA (5'-D(P*AP*AP*AP*A)-3')
ZD: capsid protein F
AE: spike protein G
BE: DNA-binding protein J
CE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
5: DNA (5'-D(P*AP*AP*AP*A)-3')
DE: capsid protein F
EE: spike protein G
FE: DNA-binding protein J
GE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
6: DNA (5'-D(P*AP*AP*AP*A)-3')
HE: capsid protein F
IE: spike protein G
JE: DNA-binding protein J
KE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
7: DNA (5'-D(P*AP*AP*AP*A)-3')
LE: capsid protein F
ME: spike protein G
NE: DNA-binding protein J
OE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
8: DNA (5'-D(P*AP*AP*AP*A)-3')
PE: capsid protein F
QE: spike protein G
RE: DNA-binding protein J
SE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
9: DNA (5'-D(P*AP*AP*AP*A)-3')
TE: capsid protein F
UE: spike protein G
VE: DNA-binding protein J
WE: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
aA: DNA (5'-D(P*AP*AP*AP*A)-3')
XE: capsid protein F
YE: spike protein G
ZE: DNA-binding protein J
AF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
bA: DNA (5'-D(P*AP*AP*AP*A)-3')
BF: capsid protein F
CF: spike protein G
DF: DNA-binding protein J
EF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
cA: DNA (5'-D(P*AP*AP*AP*A)-3')
FF: capsid protein F
GF: spike protein G
HF: DNA-binding protein J
IF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
dA: DNA (5'-D(P*AP*AP*AP*A)-3')
JF: capsid protein F
KF: spike protein G
LF: DNA-binding protein J
MF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
eA: DNA (5'-D(P*AP*AP*AP*A)-3')
NF: capsid protein F
OF: spike protein G
PF: DNA-binding protein J
QF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
fA: DNA (5'-D(P*AP*AP*AP*A)-3')
RF: capsid protein F
SF: spike protein G
TF: DNA-binding protein J
UF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
gA: DNA (5'-D(P*AP*AP*AP*A)-3')
VF: capsid protein F
WF: spike protein G
XF: DNA-binding protein J
YF: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
hA: DNA (5'-D(P*AP*AP*AP*A)-3')
ZF: capsid protein F
AG: spike protein G
BG: DNA-binding protein J
CG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
iA: DNA (5'-D(P*AP*AP*AP*A)-3')
DG: capsid protein F
EG: spike protein G
FG: DNA-binding protein J
GG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
jA: DNA (5'-D(P*AP*AP*AP*A)-3')
HG: capsid protein F
IG: spike protein G
JG: DNA-binding protein J
KG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
kA: DNA (5'-D(P*AP*AP*AP*A)-3')
LG: capsid protein F
MG: spike protein G
NG: DNA-binding protein J
OG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
lA: DNA (5'-D(P*AP*AP*AP*A)-3')
PG: capsid protein F
QG: spike protein G
RG: DNA-binding protein J
SG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
mA: DNA (5'-D(P*AP*AP*AP*A)-3')
TG: capsid protein F
UG: spike protein G
VG: DNA-binding protein J
WG: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
nA: DNA (5'-D(P*AP*AP*AP*A)-3')
XG: capsid protein F
YG: spike protein G
ZG: DNA-binding protein J
AH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
oA: DNA (5'-D(P*AP*AP*AP*A)-3')
BH: capsid protein F
CH: spike protein G
DH: DNA-binding protein J
EH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
pA: DNA (5'-D(P*AP*AP*AP*A)-3')
FH: capsid protein F
GH: spike protein G
HH: DNA-binding protein J
IH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
qA: DNA (5'-D(P*AP*AP*AP*A)-3')
JH: capsid protein F
KH: spike protein G
LH: DNA-binding protein J
MH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
rA: DNA (5'-D(P*AP*AP*AP*A)-3')
NH: capsid protein F
OH: spike protein G
PH: DNA-binding protein J
QH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
sA: DNA (5'-D(P*AP*AP*AP*A)-3')
RH: capsid protein F
SH: spike protein G
TH: DNA-binding protein J
UH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
tA: DNA (5'-D(P*AP*AP*AP*A)-3')
VH: capsid protein F
WH: spike protein G
XH: DNA-binding protein J
YH: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
uA: DNA (5'-D(P*AP*AP*AP*A)-3')
ZH: capsid protein F
AI: spike protein G
BI: DNA-binding protein J
CI: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
vA: DNA (5'-D(P*AP*AP*AP*A)-3')
DI: capsid protein F
EI: spike protein G
FI: DNA-binding protein J
GI: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
wA: DNA (5'-D(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)4,376,473300
Polymers4,376,473300
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


Mass: 48418.332 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Salmonella phage PJNS002 (virus)
#2: Protein ...
spike protein G


Mass: 18864.549 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Salmonella phage PJNS002 (virus)
#3: Protein/peptide ...
DNA-binding protein J


Mass: 2929.386 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Salmonella phage PJNS002 (virus)
#4: DNA chain ...
DNA (5'-D(P*AP*AP*AP*AP*A)-3')


Mass: 1521.077 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Salmonella phage PJNS002 (virus)
#5: DNA chain ...
DNA (5'-D(P*AP*AP*AP*A)-3')


Mass: 1207.870 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Salmonella phage PJNS002 (virus)
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: #1-#3 / Source: NATURAL
Molecular weightValue: 4.31 MDa / Experimental value: NO
Source (natural)Organism: Salmonella phage PJNS002 (virus)
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: 3827
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: 528658
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86486 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 18.15 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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