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- EMDB-25396: Goslar chimallin C1 localized reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-25396
TitleGoslar chimallin C1 localized reconstruction
Map data
Sample
  • Complex: Goslar chimallin C1 localized reconstruction
    • Protein or peptide: Chimallin
  • Ligand: water
Keywordsphage / viral protein / STRUCTURAL PROTEIN
Function / homologyhost cell cytoplasm / Chimallin
Function and homology information
Biological speciesGoslarvirus / Escherichia phage vB_EcoM_Goslar (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsLaughlin TG / Deep A / Prichard AM / Seitz C / Gu Y / Enustun E / Suslov S / Khanna K / Birkholz EA / Amaro RE ...Laughlin TG / Deep A / Prichard AM / Seitz C / Gu Y / Enustun E / Suslov S / Khanna K / Birkholz EA / Amaro RE / Pogliano J / Corbett KD / Villa E
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM129245 United States
National Science Foundation (NSF, United States)NSF DBI 1920374 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI148814 United States
CitationJournal: Nature / Year: 2022
Title: Architecture and self-assembly of the jumbo bacteriophage nuclear shell.
Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie ...Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie E Amaro / Joe Pogliano / Kevin D Corbett / Elizabeth Villa /
Abstract: Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a ...Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
History
DepositionNov 6, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25396.png

Downloads & links

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Map

FileDownload / File: emd_25396.map.gz / Format: CCP4 / Size: 416.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 478 pix.
= 473.311 Å		0.99 Å/pix.
x 478 pix.
= 473.311 Å		0.99 Å/pix.
x 478 pix.
= 473.311 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99019 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.3157523 - 3.4472334
Average (Standard dev.)0.0018339744 (±0.028693803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions478478478
Spacing478478478
CellA=B=C: 473.31082 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25396_msk_1.map
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Additional map: sharpened, upsampled, cropped

Fileemd_25396_additional_1.map
Annotationsharpened, upsampled, cropped
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Half map: #1

Fileemd_25396_half_map_1.map
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Half map: #2

Fileemd_25396_half_map_2.map
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Sample components

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Entire : Goslar chimallin C1 localized reconstruction

EntireName: Goslar chimallin C1 localized reconstruction
Components
  • Complex: Goslar chimallin C1 localized reconstruction
    • Protein or peptide: Chimallin
  • Ligand: water

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Supramolecule #1: Goslar chimallin C1 localized reconstruction

SupramoleculeName: Goslar chimallin C1 localized reconstruction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Goslarvirus

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Macromolecule #1: Chimallin

MacromoleculeName: Chimallin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoM_Goslar (virus)
Molecular weightTheoretical: 69.889445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMGLDVRN NGNDNVEIRA AETRTAQRAD EALETAADFA GQPKVTHTMR TINRTLSRRI SRNTGSEQVL NLRRLMEKYL EDTRFKDDF IFVAVDPNQY SVPYPTLVVM SGAKVGDHNH FFGYVLPLVA GLAPLPRREE QGPHGNILVP RTWVDNLNGT F INEVMAAM ...String:
SNAMGLDVRN NGNDNVEIRA AETRTAQRAD EALETAADFA GQPKVTHTMR TINRTLSRRI SRNTGSEQVL NLRRLMEKYL EDTRFKDDF IFVAVDPNQY SVPYPTLVVM SGAKVGDHNH FFGYVLPLVA GLAPLPRREE QGPHGNILVP RTWVDNLNGT F INEVMAAM YAAIGGKSNG TARIAGLAVV TNEITAESAH LATTLLSAAD NAIQTAIEIR LGDKLGLPQF NLGMMASDQP IS SVQYNTS GMQDSDIVGN PVRSDITVTI SNRIRQAMSD YDSQQRLVAT TGYIDLTYSP QNPTFNQGPV LVNGYPVPPT VQY QPRYVM TSAYPLELDA FTPNTFVLGL IGTIATLNSG MAWAQSLISN AARGIGPHNP GALAMVLDPE VTAPLDLSTQ TNEQ IYKFL QQVLYPSLLI SIDVPEEGEY SWLLRMIPAA EKIYTGKVEG EVREISEGYK ALYRAFDDVT LGCFSKKYQY GLPLV YATG NRIPLGHYNH QDGHRHDIRD MDDLYMMNIT NPDTVEAWED SFDRTDMTMS QRVVARHEII DRVLSGSWEQ TGWAMR YDF DPLALQALIE AAADAGFTIR PENIQHLAGT AVRGNMAARA RGLGNISGNI YARSDRPNVG VNNMGGAFNL F

UniProtKB: Chimallin

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 20 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3192 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1407340 / Details: Initial sub-particle count
Startup modelType of model: OTHER / Details: sub-volume of parent map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1407340
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 78
Output model

PDB-7sqv:
Goslar chimallin C1 localized reconstruction

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