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- PDB-9zbs: The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:col... -

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Basic information

Entry
Database: PDB / ID: 9zbs
TitleThe cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)
Components
  • Head to Tail protein gp72
  • Head-tail joining protein
  • Portal protein
  • Tail completion protein
KeywordsVIRAL PROTEIN / Pakpunavirus P7-1 / Cryo-EM / in situ / structure / neck / portal protein / H-t-T / collar protein / gateway protein
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 neck (portal:H-t-T:collar:gateway)
Authors: Li, F. / Cingolani, G.
History
DepositionNov 21, 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

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
M: Head to Tail protein gp72
N: Head to Tail protein gp72
O: Head to Tail protein gp72
P: Head to Tail protein gp72
Q: Head to Tail protein gp72
R: Head to Tail protein gp72
S: Head to Tail protein gp72
T: Head to Tail protein gp72
U: Head to Tail protein gp72
V: Head to Tail protein gp72
W: Head to Tail protein gp72
X: Head to Tail protein gp72
Y: Head-tail joining protein
Z: Head-tail joining protein
a: Head-tail joining protein
b: Head-tail joining protein
c: Head-tail joining protein
d: Head-tail joining protein
e: Tail completion protein
f: Tail completion protein
g: Tail completion protein
h: Tail completion protein
i: Tail completion protein
j: Tail completion protein


Theoretical massNumber of molelcules
Total (without water)1,084,11136
Polymers1,084,11136
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

#1: Protein
Portal protein


Mass: 54362.641 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#2: Protein
Head to Tail protein gp72


Mass: 18142.607 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#3: Protein
Head-tail joining protein


Mass: 14369.471 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
#4: Protein
Tail completion protein


Mass: 21305.135 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pakpunavirus
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: COMPLEX / Entity ID: #1, #4, #3, #2 / Source: NATURAL
Source (natural)Organism: Pakpunavirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
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: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D 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_d0.00473824
ELECTRON MICROSCOPYf_angle_d0.51999576
ELECTRON MICROSCOPYf_dihedral_angle_d12.53628566
ELECTRON MICROSCOPYf_chiral_restr0.0410548
ELECTRON MICROSCOPYf_plane_restr0.00513140

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