[English] 日本語
Yorodumi
- EMDB-25392: 201phi2-1 Chimallin C1 localized reconstruction -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25392
Title201phi2-1 Chimallin C1 localized reconstruction
Map data
Sample
  • Complex: 201phi2-1 chimallin C1 localized reconstruction
    • Protein or peptide: Chimallin
Keywordsphage / viral protein / STRUCTURAL PROTEIN
Function / homologyhost cell cytoplasm / Chimallin
Function and homology information
Biological speciesPseudomonas phage 201phi2-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

-
Structure visualization

Supplemental images

emd_25392.png

Downloads & links

-
Map

FileDownload / File: emd_25392.map.gz / Format: CCP4 / Size: 105.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 302 pix.
= 408.5 Å		1.35 Å/pix.
x 302 pix.
= 408.5 Å		1.35 Å/pix.
x 302 pix.
= 408.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35265 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.4385512 - 2.951494
Average (Standard dev.)0.009518194 (±0.04364909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions302302302
Spacing302302302
CellA=B=C: 408.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_25392_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened, reboxed

Fileemd_25392_additional_1.map
Annotationsharpened, reboxed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25392_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25392_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 201phi2-1 chimallin C1 localized reconstruction

EntireName: 201phi2-1 chimallin C1 localized reconstruction
Components
  • Complex: 201phi2-1 chimallin C1 localized reconstruction
    • Protein or peptide: Chimallin

-
Supramolecule #1: 201phi2-1 chimallin C1 localized reconstruction

SupramoleculeName: 201phi2-1 chimallin C1 localized reconstruction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage 201phi2-1 (virus)

-
Macromolecule #1: Chimallin

MacromoleculeName: Chimallin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 2657452
Details: Sub-particle count after expansion of C4 parent particle set
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2657452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 108
Output model

PDB-7sqs:
201phi2-1 Chimallin C1 localized reconstruction

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more