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- PDB-9d93: Mycobacteriophage Bxb1 tail tip - Composite map and model -

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Basic information

Entry
Database: PDB / ID: 9d93
TitleMycobacteriophage Bxb1 tail tip - Composite map and model
Components
  • (Minor tail protein) x 8
  • Major tail protein
  • Tapemeasure protein
KeywordsVIRAL PROTEIN / Bacteriophage / tail tip
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Fibronectin type III / Beta-lactamase/transpeptidase-like / Immunoglobulin-like fold
Similarity search - Domain/homology
Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Minor tail protein / Tapemeasure protein / Major tail protein / Minor tail protein
Similarity search - Component
Biological speciesMycobacterium phage Bxb1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsFreeman, K.G.
Funding support United States, Taiwan, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI173544 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116884 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorS10 OD025009 United States
National Institutes of Health/Office of the DirectorS10 OD019995 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
Academia Sinica (Taiwan)AS-IDR-110-06 Taiwan
CitationJournal: To Be Published
Title: Structure and infection dynamics of mycobacteriophage Bxb1
Authors: Freeman, K.G. / Mondal, S. / Macale, L.S. / Podgorski, J. / White, S.J. / Silva, B. / Ortiz, V. / Huet, A. / Narsico, J.T. / Ho, M.C. / Jacobs-Sera, D. / Lowary, T.L. / Conway, J.F. / Park, D. / Hatfull, G.F.
History
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ja: Major tail protein
Jb: Major tail protein
Jc: Major tail protein
Jd: Major tail protein
Je: Major tail protein
Jf: Major tail protein
Ka: Minor tail protein
Kb: Minor tail protein
Kc: Minor tail protein
La: Minor tail protein
Lb: Minor tail protein
Lc: Minor tail protein
Ld: Minor tail protein
Le: Minor tail protein
Lf: Minor tail protein
Lg: Minor tail protein
Lh: Minor tail protein
Li: Minor tail protein
Ma: Minor tail protein
Mb: Minor tail protein
Mc: Minor tail protein
Md: Minor tail protein
Me: Minor tail protein
Mf: Minor tail protein
Na: Tapemeasure protein
Nb: Tapemeasure protein
Nc: Tapemeasure protein
Oa: Minor tail protein
Ob: Minor tail protein
Oc: Minor tail protein
Pa: Minor tail protein
Pb: Minor tail protein
Pc: Minor tail protein
Qa: Minor tail protein
Qb: Minor tail protein
Qc: Minor tail protein
Ra: Minor tail protein
Rb: Minor tail protein
Rc: Minor tail protein
Rd: Minor tail protein
Re: Minor tail protein
Rf: Minor tail protein
Sa: Minor tail protein
Sb: Minor tail protein
Sc: Minor tail protein


Theoretical massNumber of molelcules
Total (without water)1,941,66645
Polymers1,941,66645
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, 45 molecules JaJbJcJdJeJfKaKbKcLaLbLcLdLeLfLgLhLiMaMbMcMdMeMfNaNbNcOaObOc...

#1: Protein
Major tail protein


Mass: 30170.271 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A2
#2: Protein Minor tail protein


Mass: 9696.724 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: A0A345MFL2
#3: Protein
Minor tail protein


Mass: 36723.973 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0B7
#4: Protein
Minor tail protein


Mass: 74357.398 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B098
#5: Protein Tapemeasure protein


Mass: 84842.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B099
#6: Protein Minor tail protein


Mass: 67065.172 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B096
#7: Protein Minor tail protein


Mass: 64056.230 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B092
#8: Protein Minor tail protein


Mass: 24772.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B088
#9: Protein
Minor tail protein


Mass: 11315.524 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: A0A345MFN8
#10: Protein Minor tail protein


Mass: 54931.043 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B091

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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: Mycobacterium phage Bxb1 / Type: VIRUS
Details: Tail tip complex of Bxb1, containing ten protein subunit types. This is a composite map, and related entries for consensus and locally refined maps are noted.
Entity ID: all / Source: NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21YES
Source (natural)Organism: Mycobacterium phage Bxb1 (virus) / Strain: Mycobacterium phage Bxb1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Mycolicibacterium smegmatis MC2 155
Virus shellName: Mycobacteriophage Bxb1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
21 mMMagnesium sulfateMgSO41
368.44 mMSodium chlorideNaCl1
41 mMCalcium chlorideCaCl21
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 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 defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22280 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005103878
ELECTRON MICROSCOPYf_angle_d0.644141916
ELECTRON MICROSCOPYf_dihedral_angle_d6.12714335
ELECTRON MICROSCOPYf_chiral_restr0.04715836
ELECTRON MICROSCOPYf_plane_restr0.00618732

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