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- EMDB-40674: Subtomogram average of immature PhiKZ Major Capsid Protein from t... -

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Basic information

Entry
Database: EMDB / ID: EMD-40674
TitleSubtomogram average of immature PhiKZ Major Capsid Protein from tubular arrays
Map data
Sample
  • Complex: Immature PhiKZ major capsid protein in a tubular array
    • Protein or peptide: PhiKZ major capsid protein
Keywordsmajor capsid protein / HK97-fold / VIRAL PROTEIN
Function / homologyPHIKZ120
Function and homology information
Biological speciesPhikzvirus phiKZ
Methodsubtomogram averaging / cryo EM / Resolution: 13.0 Å
AuthorsLaughlin TG / Villa E
Funding support United States, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129245 United States
National Science Foundation (NSF, United States)NSF DBI 1920374 United States
Simons Foundation United States
CitationJournal: To Be Published
Title: A mobile intron of PhiPA3 inhibits virogenesis of co-infecting phage PhiKZ
Authors: Birkholz EA / Morgan C / Lau RK / Laughlin TG / Rangarajan S / Armbruster E / Prichard A / Meza GN / Suslov S / Meyer JR / Villa E / Corbett KD / Pogliano J
History
DepositionMay 1, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40674.png

Downloads & links

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Map

FileDownload / File: emd_40674.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.457 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.28038615 - 0.38181207
Average (Standard dev.)0.00208719 (±0.093099475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 442.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40674_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40674_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40674_half_map_2.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 : Immature PhiKZ major capsid protein in a tubular array

EntireName: Immature PhiKZ major capsid protein in a tubular array
Components
  • Complex: Immature PhiKZ major capsid protein in a tubular array
    • Protein or peptide: PhiKZ major capsid protein

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Supramolecule #1: Immature PhiKZ major capsid protein in a tubular array

SupramoleculeName: Immature PhiKZ major capsid protein in a tubular array
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Phikzvirus phiKZ

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Macromolecule #1: PhiKZ major capsid protein

MacromoleculeName: PhiKZ major capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
SequenceString: MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSSD PQVRAREERV RENQITAATM AAIACADETK YIRALRGITK AKASNEDHVK VVQHQFNGPA GGIQVFENGV GLENYNEKSQ ...String:
MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSSD PQVRAREERV RENQITAATM AAIACADETK YIRALRGITK AKASNEDHVK VVQHQFNGPA GGIQVFENGV GLENYNEKSQ RDFRVVTIGY NLAASRQDEF AERIYPTTVI NPIEGGVVQV LPYIAVMKDV YHEVSGVKMD NEEVNMVEAY RDPSILDDES IALIPALDPA GSNADFFVDP ALVPPYTIKN EQNLTITTAP LKANVRLDLM GNSNANLLIQ RGMLEVSDTI DPAGRLKNLF VLLGGKVVKF KVDRLPRAVF QPDLVGDTRN AVIRFDSDDL VVSGDTTFID GSADGVINDL KTAKLSLRLS VGFGGTISLS KGDSKFGATD TYVDKVLNED GQVMDNADPA VKAILDQLTD LAVIGFELDT RFTNTNRRQR GHLLQTRALQ FRHPIPMHAP VTLPMDTMTD EGPGEVVKAL TVNTNIRNSN NAVKRMLNYL AQLREVVHNG YNRPKFGIIE GALSAVMRPT YRYKELDLEK VIDTIKSKDR WDDVCAAILN CVKAELFPAH RDSNIEAAFR VISGNQDETP MYLFCSDKEI ANYLMTKGDD RTLGAYLKYD IVSTNNQLFD GKLVVIPTRA VQQENDILSW GQFFYVSTVI ADLPITRGGH QVTREIAAIP FNLHVNNIPF ALEFKITGFQ KVMGETQFNG KLADLKP

UniProtKB: PHIKZ120

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsP. aeruginosa cells expressing PhiPA3 gp210-GFPmut1 infected with PhiKZ

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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 / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1 / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 14 / Number images used: 60000 / Software: (Name: Dynamo (ver. 1.1514), Warp (ver. 1.09))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number subtomograms used: 21121
FSC plot (resolution estimation)

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