[English] 日本語
Yorodumi
- EMDB-43792: phi29 empty capsid lacking pentons and portal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43792
Titlephi29 empty capsid lacking pentons and portal
Map dataphi29 capsid with no pentons or portal
Sample
  • Virus: Baccilus phage phi29 (bacteria)
Keywordsbacteriophage / prohead / HK97 fold / VIRUS / VIRUS LIKE PARTICLE
Biological speciesBaccilus phage phi29 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsWoodson ME / Morais MC / Seth S / Zhang W / Jardine PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 United States
CitationJournal: Sci Adv / Year: 2025
Title: Phi29 assembly intermediates reveal how scaffold interactions with capsid protein drive capsid construction and maturation.
Authors: Michael Woodson / Nikolai S Prokhorov / Seth D Scott / Wei Zhao / Wei Zhang / Kyung H Choi / Paul J Jardine / Marc C Morais /
Abstract: The self-assembly of bacteriophage capsids from major capsid proteins (MCPs) and scaffolding proteins (SPs) and the subsequent expansion of these capsids are essential steps in bacteriophage life ...The self-assembly of bacteriophage capsids from major capsid proteins (MCPs) and scaffolding proteins (SPs) and the subsequent expansion of these capsids are essential steps in bacteriophage life cycles. However, the mechanism by which assembly occurs remains poorly understood, and few intermediate states are available to illuminate the expansion of meta-stable procapsids into robust mature capsids. Here, we present the structure of a partially expanded phi29 procapsid that reveals distinct conformations of MCPs and allows visualization of SPs in multiple oligomeric states. These results suggest that formation of SP dimers, tetramers, and higher-order oligomers drives dissociation of SP from MCP to actuate capsid expansion. Hexons expand first, and we propose penton maturation is delayed by a symmetry match with SP oligomers. We further show that the prolate shape of phi29's capsid is possible due to concave hexons in the equatorial region of the capsid that may alter interactions with SP and explain the observed dependence of the prolate shape on SP.
History
DepositionFeb 23, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43792.png

Downloads & links

-
Map

FileDownload / File: emd_43792.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphi29 capsid with no pentons or portal
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 900 pix.
= 997.2 Å		1.11 Å/pix.
x 900 pix.
= 997.2 Å		1.11 Å/pix.
x 900 pix.
= 997.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0128
Minimum - Maximum-0.07677105 - 0.11165122
Average (Standard dev.)0.00015568732 (±0.0027091822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions900900900
Spacing900900900
CellA=B=C: 997.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_43792_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43792_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Baccilus phage phi29

EntireName: Baccilus phage phi29 (bacteria)
Components
  • Virus: Baccilus phage phi29 (bacteria)

-
Supramolecule #1: Baccilus phage phi29

SupramoleculeName: Baccilus phage phi29 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 884424 / Sci species name: Baccilus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Bacillus subtilis (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 35.0 Å / T number (triangulation number): 3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
5.0 mMMgCl2magnesium chloride
50.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 27412
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

+
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