[English] 日本語
Yorodumi
- EMDB-40271: Mycobacterium phage Adjutor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40271
TitleMycobacterium phage Adjutor
Map dataSharpened map of ewald sphere corrected postprocess.
Sample
  • Virus: Mycobacterium phage Adjutor (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: gp_16 (Minor Capsid Protein)
    • Protein or peptide: HNH endonuclease
KeywordsT=7 / HK97 / Tailed bacteriophage / Capsid / VIRUS
Function / homologyUncharacterized protein / Capsid decoration protein / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Adjutor (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsPodgorski JM / White SJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids.
Authors: Jennifer M Podgorski / Joshua Podgorski / Lawrence Abad / Deborah Jacobs-Sera / Krista G Freeman / Colin Brown / Graham F Hatfull / Antoni Luque / Simon J White /
Abstract: Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the ...Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the HK97-fold. The high density of the genome exerts an internal pressure, requiring a maturation process that reinforces their capsids. However, it is unclear how capsid stabilization strategies have adapted to accommodate the evolution of larger genomes in this virus group. Here we characterize a capsid reinforcement mechanism in two evolutionary-related actinobacteriophages that modifies the length of a stabilization protein to accommodate a larger genome while maintaining the same capsid size. We use cryo-EM to reveal that capsids contain split hexamers of HK97-fold proteins with a stabilization protein in the chasm. The observation of split hexamers in mature capsids is unprecedented, so we rationalize this result mathematically, discovering that icosahedral capsids can be formed by all split or skewed hexamers as long as their T-number is not a multiple of three. Our results suggest that analogous stabilization mechanisms can be present in other icosahedral capsids, and they provide a strategy for engineering capsids accommodating larger DNA cargoes as gene delivery systems.
History
DepositionApr 1, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40271.png

Downloads & links

-
Map

FileDownload / File: emd_40271.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected postprocess.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.2 Å/pix.
x 800 pix.
= 960. Å		1.2 Å/pix.
x 800 pix.
= 960. Å		1.2 Å/pix.
x 800 pix.
= 960. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-10.170918 - 22.292313
Average (Standard dev.)-0.000000000001745 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 960.00006 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_40271_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Ewald sphere corrected map.

Fileemd_40271_additional_1.map
AnnotationEwald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of ewald sphere corrected map.

Fileemd_40271_half_map_1.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of ewald sphere corrected map.

Fileemd_40271_half_map_2.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mycobacterium phage Adjutor

EntireName: Mycobacterium phage Adjutor (virus)
Components
  • Virus: Mycobacterium phage Adjutor (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: gp_16 (Minor Capsid Protein)
    • Protein or peptide: HNH endonuclease

-
Supramolecule #1: Mycobacterium phage Adjutor

SupramoleculeName: Mycobacterium phage Adjutor / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 528321 / Sci species name: Mycobacterium phage Adjutor / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / Diameter: 750.0 Å / T number (triangulation number): 7

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 45.525645 KDa
SequenceString: MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER ...String:
MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER EADIEGLPYK VYPLYNGDNM IPPEYNGTTF STGHNHYLVS GGTKIDSADV EMAADHIREH GYTEENGTQL IA FAHKAEI QEVRRFRFGQ TNNNSAVANY DFVQSQGESP LYLPNADGLL GKQPQSMWKG LRVKGSYDDV LWIEEPTMPA GYV LFLATG GTLAQQNLVG LREHEDAAWR GLRQIPGNQT RYPLIDSFYQ RSFGTGIRQR GGAVVLQIKA SGTYDIPTKW TNGG GFE

UniProtKB: Major capsid protein

-
Macromolecule #2: gp_16 (Minor Capsid Protein)

MacromoleculeName: gp_16 (Minor Capsid Protein) / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 13.766352 KDa
SequenceString:
MARYDKYNPY GGGFRAPLAA DWTDADAGKL YAVGINNVGA VVKGAGQSGV AGVLVLTKGA KAGSIVDVMK FGEVVEFGPT SGTPGTDFG AAGTAYYADT STGAINSTSG EAKVKVGHTV GAQRLIVAVA DGVVDPSPAA

UniProtKB: Capsid decoration protein

-
Macromolecule #3: HNH endonuclease

MacromoleculeName: HNH endonuclease / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Adjutor (virus)
Molecular weightTheoretical: 6.198103 KDa
SequenceString:
MAKGVKKLPK RKGTNPIPRD KWNSDDIARR QLEQDQKLHL TTKGPHTGTN DSFK

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 6664 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL / Details: Relion SGD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 44239
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsAmino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde.
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8saj:
Mycobacterium phage Adjutor

+
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