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- PDB-9zd8: The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended ... -

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Basic information

Entry
Database: PDB / ID: 9zd8
TitleThe cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
Components
  • (gp88) x 2
  • gp78
  • gp79
  • gp83
  • gp84
  • gp85
  • gp86
  • gp87
  • gp89
KeywordsVIRAL PROTEIN / Pakpunavirus P7-1 / Cryo-EM / in situ / structure / baseplate
Biological speciesPakpunavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi, F. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
Authors: Li, F. / Cingolani, G.
History
DepositionNov 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data 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
0: gp88
1: gp89
A: gp83
B: gp83
C: gp83
D: gp83
E: gp83
F: gp83
G: gp79
H: gp78
I: gp84
K: gp87
L: gp88
M: gp88
N: gp88
O: gp89
P: gp86
Q: gp79
R: gp78
S: gp84
U: gp87
V: gp88
W: gp88
X: gp88
Y: gp89
Z: gp86
a: gp79
b: gp78
c: gp84
e: gp87
f: gp88
g: gp88
h: gp88
i: gp89
j: gp86
k: gp79
l: gp78
m: gp84
n: gp87
o: gp88
p: gp89
q: gp79
r: gp78
s: gp84
t: gp87
u: gp88
v: gp89
w: gp79
x: gp78
y: gp84
z: gp87
J: gp85
T: gp85
d: gp85
4: gp88
2: gp88
3: gp88
5: gp88
6: gp88
7: gp88
8: gp88
9: gp88
AA: gp88


Theoretical massNumber of molelcules
Total (without water)2,301,75563
Polymers2,301,75563
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 63 molecules 0LMNVWXfghou1OYipvABCDEFGQakqw...

#1: Protein
gp88


Mass: 52425.945 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#2: Protein
gp89


Mass: 26698.064 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#3: Protein
gp83


Mass: 28575.006 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#4: Protein
gp79


Mass: 17714.852 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#5: Protein
gp78


Mass: 18265.016 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#6: Protein
gp84


Mass: 14001.813 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#7: Protein
gp87


Mass: 14196.220 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#8: Protein gp86


Mass: 26712.225 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#9: Protein gp85


Mass: 33881.938 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#10: Protein
gp88


Mass: 86017.289 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus

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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: Pakpunavirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pakpunavirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.21.2_5419model refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10400 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003109794
ELECTRON MICROSCOPYf_angle_d0.487149466
ELECTRON MICROSCOPYf_dihedral_angle_d13.02540137
ELECTRON MICROSCOPYf_chiral_restr0.04417433
ELECTRON MICROSCOPYf_plane_restr0.00419533

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