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- PDB-8xan: Major tail protein of SH-Ab15497 -

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Basic information

Entry
Database: PDB / ID: 8xan
TitleMajor tail protein of SH-Ab15497
ComponentsMajor tail structural protein
KeywordsVIRAL PROTEIN / helical reconstruction / C3 symmetry
Function / homologyPhage tail tube protein-like / Phage tail tube protein / Major tail structural protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 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: Major tail protein of SH-Ab15497
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

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Assembly

Deposited unit
B: Major tail structural protein
A: Major tail structural protein
C: Major tail structural protein


Theoretical massNumber of molelcules
Total (without water)99,6253
Polymers99,6253
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 Major tail structural protein


Mass: 33208.465 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage SH-Ab 15497 (virus) / References: UniProt: A0A2H5BHH8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical 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
Virus shellDiameter: 650 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
28 mMmagnesium sulfateMgSO41
350 mMTris-HCl1
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: FEI TITAN 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
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 40.7 ° / Axial rise/subunit: 38.3 Å / Axial symmetry: C3
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157605 / Symmetry type: HELICAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067089
ELECTRON MICROSCOPYf_angle_d0.9569624
ELECTRON MICROSCOPYf_dihedral_angle_d4.798981
ELECTRON MICROSCOPYf_chiral_restr0.0461134
ELECTRON MICROSCOPYf_plane_restr0.0051245

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