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- PDB-9d9w: Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model -

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Basic information

Entry
Database: PDB / ID: 9d9w
TitleMycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model
Components
  • Major capsid protein
  • Portal protein
KeywordsVIRAL PROTEIN / Bacteriophage / Mycobacteriophage Bxb1 / capsid / portal / VIRUS
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / Phage capsid / Phage capsid family / Major capsid protein / Portal protein
Function and homology information
Biological speciesMycobacterium phage Bxb1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: Major capsid protein
Ab: Major capsid protein
Ac: Major capsid protein
Ad: Major capsid protein
Ae: Major capsid protein
Af: Major capsid protein
Ba: Major capsid protein
Bb: Major capsid protein
Bc: Major capsid protein
Bd: Major capsid protein
Be: Major capsid protein
Bf: Major capsid protein
Ca: Major capsid protein
Cb: Major capsid protein
Cc: Major capsid protein
Cd: Major capsid protein
Ce: Major capsid protein
Cf: Major capsid protein
Da: Major capsid protein
Db: Major capsid protein
Dc: Major capsid protein
Dd: Major capsid protein
De: Major capsid protein
Df: Major capsid protein
Ea: Major capsid protein
Eb: Major capsid protein
Ec: Major capsid protein
Ed: Major capsid protein
Ee: Major capsid protein
Ef: Major capsid protein
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


Theoretical massNumber of molelcules
Total (without water)1,902,12942
Polymers1,902,12942
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 ...
Major capsid protein


Mass: 41875.461 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Bxb1 (virus) / References: UniProt: Q9B0A7
#2: 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
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: 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: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 33132 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006133098
ELECTRON MICROSCOPYf_angle_d0.695181460
ELECTRON MICROSCOPYf_dihedral_angle_d6.2518457
ELECTRON MICROSCOPYf_chiral_restr0.04520807
ELECTRON MICROSCOPYf_plane_restr0.00623804

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