[English] 日本語
Yorodumi
- EMDB-24720: SaPIbov5 procapsid structure including size redirecting protein Ccm -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24720
TitleSaPIbov5 procapsid structure including size redirecting protein Ccm
Map data
Sample
  • Complex: SaPIbov5 procapsid
    • Protein or peptide: Cos capsid morphogenesis protein (Ccm)
    • Protein or peptide: Major capsid protein
KeywordsHK97-like fold / capsid size redirection / major capsid protein / VIRUS
Function / homology
Function and homology information


ATP-dependent peptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity
Similarity search - Function
Phage capsid / Phage capsid family / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHawkins NC / Kizziah JL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI132977 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Nat Commun / Year: 2021
Title: Shape shifter: redirection of prolate phage capsid assembly by staphylococcal pathogenicity islands.
Authors: N'Toia C Hawkins / James L Kizziah / José R Penadés / Terje Dokland /
Abstract: Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects ...Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects the assembly of ϕ12 helper capsids from prolate to isometric. This size and shape shift is dependent on the SaPIbov5-encoded protein Ccm, a homolog of the ϕ12 capsid protein (CP). Using cryo-electron microscopy, we have determined structures of prolate ϕ12 procapsids and isometric SaPIbov5 procapsids. ϕ12 procapsids have icosahedral end caps with T = 4 architecture and a T = 14 cylindrical midsection, whereas SaPIbov5 procapsids have T = 4 icosahedral architecture. We built atomic models for CP and Ccm, and show that Ccm occupies the pentameric capsomers in the isometric SaPIbov5 procapsids, suggesting that preferential incorporation of Ccm pentamers prevents the cylindrical midsection from forming. Our results highlight that pirate elements have evolved diverse mechanisms to suppress phage multiplication, including the acquisition of phage capsid protein homologs.
History
DepositionAug 20, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7rwz
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rwz
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24720.png

Downloads & links

-
Map

FileDownload / File: emd_24720.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.028336255 - 0.056089107
Average (Standard dev.)0.0007578375 (±0.0039536413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z568.320568.320568.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0280.0560.001

-
Supplemental data

-
Mask #1

Fileemd_24720_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_24720_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_24720_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SaPIbov5 procapsid

EntireName: SaPIbov5 procapsid
Components
  • Complex: SaPIbov5 procapsid
    • Protein or peptide: Cos capsid morphogenesis protein (Ccm)
    • Protein or peptide: Major capsid protein

-
Supramolecule #1: SaPIbov5 procapsid

SupramoleculeName: SaPIbov5 procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

-
Macromolecule #1: Cos capsid morphogenesis protein (Ccm)

MacromoleculeName: Cos capsid morphogenesis protein (Ccm) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 40.468102 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: MKIMKEFKEQ FGYQLSNFDD MDIKGYANLY QKDIGKDVSM IEQGLKQLSI TETEVLLPEQ INKKLLGVLN MNEVNQSSNT WVGTLTKQL VSSENNFNIQ ELPTARKEVF KELLVNRELP QTLRDVITIT DDEHVESIPA LSYIKDKLAT NGIELSLNGS S KYFDRREG ...String:
MKIMKEFKEQ FGYQLSNFDD MDIKGYANLY QKDIGKDVSM IEQGLKQLSI TETEVLLPEQ INKKLLGVLN MNEVNQSSNT WVGTLTKQL VSSENNFNIQ ELPTARKEVF KELLVNRELP QTLRDVITIT DDEHVESIPA LSYIKDKLAT NGIELSLNGS S KYFDRREG HIYTEVADSV VHGSDRTLDD LLKEIFINEC VSYETTLLLD KNNASGLIDK DNQDLSLYNQ GIKEVSNTSM YD GIKQAMK DIPQTFRRKV SVVMNTEHHD KLIKELAQMG LGTLAGDLTK LFNVSHVVVT DDAQDIFVGD FGHAIYAKYE PIM YNKKKQ ALKGVYQFAL NYVFDIKIVP ELLRIVKVK

UniProtKB: Uncharacterized protein

-
Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 45.29282 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: MRNFKNDNEL LGGNEMPTLY ELKQSLGMIG QQLKNKNDEL SQKATDPNID MEDIKQLETE KAGLQQRFNI VERQVQDIEE KEKAKVKDK GEAYQSLSDN EKMVKAKAEF YRHAILPNEF EKPSMEAQRL LHALPTGNDS GGDKLLPKTL SKEIVSEPFA K NQLREKAR ...String:
MRNFKNDNEL LGGNEMPTLY ELKQSLGMIG QQLKNKNDEL SQKATDPNID MEDIKQLETE KAGLQQRFNI VERQVQDIEE KEKAKVKDK GEAYQSLSDN EKMVKAKAEF YRHAILPNEF EKPSMEAQRL LHALPTGNDS GGDKLLPKTL SKEIVSEPFA K NQLREKAR LTNIKGLEIP RVSYTLDDDD FITDVETAKE LKAKGDTVKF TTNKFKVFAA ISDTVIHGSD VDLVNWVENA LQ SGLAAKE RKDALAVSPK SGLEHMSFYN GSVKEVEGAD MYDAIINALA DLHEDYRDNA TIYMRYADYV KIISVLSNGT TNF FDTPAE KVFGKPVVFT DAAVKPIVGD FNYFGINYDG TTYDTDKDVK KGEYLFVLTA WYDQQRTLDS AFRIAKAKEN TGPL PS

UniProtKB: ATP-dependent Clp protease proteolytic subunit

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28566
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