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- EMDB-40271: Mycobacterium phage Adjutor -

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Basic information

Entry
Database: EMDB / ID: EMD-40271
TitleMycobacterium phage Adjutor
Map dataSharpened map of ewald sphere corrected postprocess.
Sample
  • Virus: Mycobacterium phage Adjutor (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: gp_16 (Minor Capsid Protein)
    • Protein or peptide: HNH endonuclease
KeywordsT=7 / HK97 / Tailed bacteriophage / Capsid / VIRUS
Function / homologyUncharacterized protein / Capsid decoration protein / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Adjutor (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsPodgorski JM / White SJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A novel accessory protein stabilizes the capsid of two actinobacteriophages
Authors: Podgorski JM / Podgorski J / Gosselin S / Abad L / Jacobs-Sera D / Brown C / Hatfull G / Gogarten P / Luque A / White SJ
History
DepositionApr 1, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40271.png

Downloads & links

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Map

FileDownload / File: emd_40271.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected postprocess.
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-10.170918 - 22.292313
Average (Standard dev.)-0.000000000001745 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 960.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40271_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ewald sphere corrected map.

Fileemd_40271_additional_1.map
AnnotationEwald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected map.

Fileemd_40271_half_map_1.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected map.

Fileemd_40271_half_map_2.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium phage Adjutor

EntireName: Mycobacterium phage Adjutor (virus)
Components
  • Virus: Mycobacterium phage Adjutor (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: gp_16 (Minor Capsid Protein)
    • Protein or peptide: HNH endonuclease

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Supramolecule #1: Mycobacterium phage Adjutor

SupramoleculeName: Mycobacterium phage Adjutor / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 528321 / Sci species name: Mycobacterium phage Adjutor / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / Diameter: 750.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 45.525645 KDa
SequenceString: MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER ...String:
MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER EADIEGLPYK VYPLYNGDNM IPPEYNGTTF STGHNHYLVS GGTKIDSADV EMAADHIREH GYTEENGTQL IA FAHKAEI QEVRRFRFGQ TNNNSAVANY DFVQSQGESP LYLPNADGLL GKQPQSMWKG LRVKGSYDDV LWIEEPTMPA GYV LFLATG GTLAQQNLVG LREHEDAAWR GLRQIPGNQT RYPLIDSFYQ RSFGTGIRQR GGAVVLQIKA SGTYDIPTKW TNGG GFE

UniProtKB: Major capsid protein

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Macromolecule #2: gp_16 (Minor Capsid Protein)

MacromoleculeName: gp_16 (Minor Capsid Protein) / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 13.766352 KDa
SequenceString:
MARYDKYNPY GGGFRAPLAA DWTDADAGKL YAVGINNVGA VVKGAGQSGV AGVLVLTKGA KAGSIVDVMK FGEVVEFGPT SGTPGTDFG AAGTAYYADT STGAINSTSG EAKVKVGHTV GAQRLIVAVA DGVVDPSPAA

UniProtKB: Capsid decoration protein

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Macromolecule #3: HNH endonuclease

MacromoleculeName: HNH endonuclease / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 6.198103 KDa
SequenceString:
MAKGVKKLPK RKGTNPIPRD KWNSDDIARR QLEQDQKLHL TTKGPHTGTN DSFK

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chlorideSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 6664 / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / Details: Relion SGD
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 44239
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsAmino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde.
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8saj:
Mycobacterium phage Adjutor

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