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- PDB-9d94: Mycobacteriophage Bxb1 portal and connector assembly - Composite ... -

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Basic information

Entry
Database: PDB / ID: 9d94
TitleMycobacteriophage Bxb1 portal and connector assembly - Composite map and model
Components
  • Head-to-tail adaptor
  • Head-to-tail stopper
  • Major tail protein
  • Portal protein
  • Tail terminator
KeywordsVIRAL PROTEIN / Bacteriophage / portal
Function / homologyMycobacteriophage D29, Gp19 / Phage protein Gp19/Gp15/Gp42 / Portal protein / Phage portal protein, SPP1 Gp6-like / Tail terminator / Major tail protein / Head-to-tail stopper / Head-to-tail adaptor / Portal protein
Function and homology information
Biological speciesMycobacterium phage Bxb1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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
Fa: Portal protein
Fb: Portal protein
Fc: Portal protein
Fd: Portal protein
Fe: Portal protein
Ff: Portal protein
Fg: Portal protein
Fh: Portal protein
Fi: Portal protein
Fj: Portal protein
Fk: Portal protein
Fl: Portal protein
Ga: Head-to-tail adaptor
Gb: Head-to-tail adaptor
Gc: Head-to-tail adaptor
Gd: Head-to-tail adaptor
Ge: Head-to-tail adaptor
Gf: Head-to-tail adaptor
Gg: Head-to-tail adaptor
Gh: Head-to-tail adaptor
Gi: Head-to-tail adaptor
Gj: Head-to-tail adaptor
Gk: Head-to-tail adaptor
Gl: Head-to-tail adaptor
Ha: Head-to-tail stopper
Hb: Head-to-tail stopper
Hc: Head-to-tail stopper
Hd: Head-to-tail stopper
He: Head-to-tail stopper
Hf: Head-to-tail stopper
Ia: Tail terminator
Ib: Tail terminator
Ic: Tail terminator
Id: Tail terminator
Ie: Tail terminator
If: Tail terminator
Ja: Major tail protein
Jb: Major tail protein
Jc: Major tail protein
Jd: Major tail protein
Je: Major tail protein
Jf: Major tail protein
Jg: Major tail protein
Jh: Major tail protein
Ji: Major tail protein
Jj: Major tail protein
Jk: Major tail protein
Jl: Major tail protein


Theoretical massNumber of molelcules
Total (without water)1,359,87448
Polymers1,359,87448
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: 53822.113 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0B0
#2: Protein
Head-to-tail adaptor


Mass: 14064.146 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A6
#3: Protein
Head-to-tail stopper


Mass: 14302.012 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A5
#4: Protein
Tail terminator


Mass: 16230.531 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: A0A345MFM5
#5: Protein
Major tail protein


Mass: 30170.271 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A2

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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: Portal and connector complex of Bxb1, containing five 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
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
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: OTHER / Num. of particles: 22590 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00393594
ELECTRON MICROSCOPYf_angle_d0.659127496
ELECTRON MICROSCOPYf_dihedral_angle_d5.54213000
ELECTRON MICROSCOPYf_chiral_restr0.04414227
ELECTRON MICROSCOPYf_plane_restr0.00616813

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