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- EMDB-25390: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-25390
Title201Phi2-1 Chimallin Cubic (O, 24mer) assembly
Map data
Sample
  • Complex: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly
    • Protein or peptide: Chimallin
KeywordsPhage / virus / STRUCTURAL PROTEIN
Function / homologyhost cell cytoplasm / Chimallin
Function and homology information
Biological speciesPseudomonas phage 201phi2-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLaughlin TG / Deep A
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129245 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_25390.png

Downloads & links

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Map

FileDownload / File: emd_25390.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 368 pix.
= 395.6 Å		1.08 Å/pix.
x 368 pix.
= 395.6 Å		1.08 Å/pix.
x 368 pix.
= 395.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.0020674337 - 0.010125051
Average (Standard dev.)0.000092223665 (±0.00085855497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 395.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25390_msk_1.map
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Half map: #1

Fileemd_25390_half_map_1.map
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Half map: #2

Fileemd_25390_half_map_2.map
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Sample components

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Entire : 201Phi2-1 Chimallin Cubic (O, 24mer) assembly

EntireName: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly
Components
  • Complex: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly
    • Protein or peptide: Chimallin

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Supramolecule #1: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly

SupramoleculeName: 201Phi2-1 Chimallin Cubic (O, 24mer) assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage 201phi2-1 (virus)
Molecular weightTheoretical: 1.67 MDa

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Macromolecule #1: Chimallin

MacromoleculeName: Chimallin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage 201phi2-1 (virus)
Molecular weightTheoretical: 69.784523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMIRDTAT NTTQTQAAPQ QAPAQQFTQA PQEKPMQSTQ SQPTPSYAGT GGINSQFTRS GNVQGGDARA SEALTVFTRL KEQAVAQQD LADDFSILRF DRDQHQVGWS SLVIAKQISL NGQPVIAVRP LILPNNSIEL PKRKTNIVNG MQTDVIESDI D VGTVFSAQ ...String:
SNAMIRDTAT NTTQTQAAPQ QAPAQQFTQA PQEKPMQSTQ SQPTPSYAGT GGINSQFTRS GNVQGGDARA SEALTVFTRL KEQAVAQQD LADDFSILRF DRDQHQVGWS SLVIAKQISL NGQPVIAVRP LILPNNSIEL PKRKTNIVNG MQTDVIESDI D VGTVFSAQ YFNRLSTYVQ NTLGKPGAKV VLAGPFPIPA DLVLKDSELQ LRNLLIKSVN ACDDILALHS GERPFTIAGL KG QQGETLA AKVDIRTQPL HDTVGNPIRA DIVVTTQRVR RNGQQENEFY ETDVKLNQVA MFTNLERTPQ AQAQTLFPNQ QQV ATPAPW VASVVITDVR NADGIQANTP EMYWFALSNA FRSTHGHAWA RPFLPMTGVA KDMKDIGALG WMSALRNRID TKAA NFDDA QFGQLMLSQV QPNPVFQIDL NRMGETAQMD SLQLDAAGGP NAQKAAATII RQINNLGGGG FERFFDHTTQ PILER TGQV IDLGNWFDGD EKRDRRDLDN LAALNAAEGN ENEFWGFYGA QLNPNLHPDL RNRQSRNYDR QYLGSTVTYT GKAERC TYN AKFIEALDRY LAEAGLQITM DNTSVLNSGQ RFMGNSVIGN NMVSGQAQVH SAYAGTQGFN TQYQTGPSSF Y

UniProtKB: Chimallin

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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

Concentration0.3 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 / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 4192 / Average electron dose: 42.6 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: 140782
Startup modelType of model: OTHER / Details: Subtomogram average
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 128798
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 408 / Target criteria: Correlation Coefficient
Output model

PDB-7sqq:
201Phi2-1 Chimallin Cubic (O, 24mer) assembly

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