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- PDB-8xb6: Portal-vertex of SH-Ab15497 in C1 symmetry -

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Basic information

Entry
Database: PDB / ID: 8xb6
TitlePortal-vertex of SH-Ab15497 in C1 symmetry
Components
  • Major capsid protein
  • Portal protein
KeywordsVIRAL PROTEIN / symmetry-mismatch
Function / homologyDomain of unknown function DUF4055 / Domain of unknown function (DUF4055) / Major capsid protein 13-like / Major capsid protein 13-like / Portal protein / Major capsid protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLin, J. / Zhao, S.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370704 China
National Natural Science Foundation of China (NSFC)32122024 China
CitationJournal: To Be Published
Title: Portal-vertex of SH-Ab15497 in C1 symmetry
Authors: Lin, J. / Zhao, S.W.
History
DepositionDec 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: 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: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Major capsid protein
R: Major capsid protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)1,026,77122
Polymers1,026,77122
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: 57059.113 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage SH-Ab 15497 (virus) / References: UniProt: A0A2H5BHC5
#2: Protein
Major capsid protein


Mass: 34206.160 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage SH-Ab 15497 (virus) / References: UniProt: A0A2H5BHF7
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: Acinetobacter phage SH-Ab 15497 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Acinetobacter phage SH-Ab 15497 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Acinetobacter baumannii
Virus shellDiameter: 650 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 27057

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72915 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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