[English] 日本語
Yorodumi
- EMDB-43145: SaPI1 portal structure in mature capsids containing DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43145
TitleSaPI1 portal structure in mature capsids containing DNA
Map data
Sample
  • Virus: Dubowvirus dv80alpha
    • Protein or peptide: Portal protein
    • Protein or peptide: Connector
Keywordsportal / phage / sapi / STRUCTURAL PROTEIN
Biological speciesDubowvirus dv80alpha
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKizziah JL / Mukherjee A / Dokland T
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD024978 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA013148 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI083255 United States
CitationJournal: J Mol Biol / Year: 2024
Title: Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation.
Authors: Amarshi Mukherjee / James L Kizziah / N'Toia C Hawkins / Mohamed O Nasef / Laura K Parker / Terje Dokland /
Abstract: Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often ...Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
History
DepositionDec 14, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43145.png

Downloads & links

-
Map

FileDownload / File: emd_43145.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0262
Minimum - Maximum-0.07388809 - 0.121682145
Average (Standard dev.)-0.00085562374 (±0.006560126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43145_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43145_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43145_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dubowvirus dv80alpha

EntireName: Dubowvirus dv80alpha
Components
  • Virus: Dubowvirus dv80alpha
    • Protein or peptide: Portal protein
    • Protein or peptide: Connector

-
Supramolecule #1: Dubowvirus dv80alpha

SupramoleculeName: Dubowvirus dv80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 53369 / Sci species name: Dubowvirus dv80alpha / Virus type: SATELLITE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dubowvirus dv80alpha
Molecular weightTheoretical: 59.55182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLKVNEFETD TDLRGNINYL FNDEANVVYT YDGTESDLLQ NVNEVSKYIE HHMDYQRPRL KVLSDYYEGK TKNLVELTRR KEEYMADNR VAHDYASYIS DFINGYFLGN PIQYQDDDKD VLEAIEAFND LNDVESHNRS LGLDLSIYGK AYELMIRNQD D ETRLYKSD ...String:
MLKVNEFETD TDLRGNINYL FNDEANVVYT YDGTESDLLQ NVNEVSKYIE HHMDYQRPRL KVLSDYYEGK TKNLVELTRR KEEYMADNR VAHDYASYIS DFINGYFLGN PIQYQDDDKD VLEAIEAFND LNDVESHNRS LGLDLSIYGK AYELMIRNQD D ETRLYKSD AMSTFIIYDN TVERNSIAGV RYLRTKPIDK TDEDEVFTVD LFTSHGVYRY LTNRTNGLKL TPRENSFESH SF ERMPITE FSNNERRKGD YEKVITLIDL YDNAESDTAN YMSDLNDAML LIKGNLNLDP VEVRKQKEAN VLFLEPTVYV DAE GRETEG SVDGGYIYKQ YDVQGTEAYK DRLNSDIHMF TNTPNMKDDN FSGTQSGEAM KYKLFGLEQR TKTKEGLFTK GLRR RAKLL ETILKNTRSI DANKDFNTVR YVYNRNLPKS LIEELKAYID SGGKISQTTL MSLFSFFQDP ELEVKKIEED EKESI KKAQ KGIYKDPRDI NDDEQDDDTK DTVDKKE

-
Macromolecule #2: Connector

MacromoleculeName: Connector / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dubowvirus dv80alpha
Molecular weightTheoretical: 12.809583 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTLADVKKR IGLKDEKQDE QLEEIIKSCE SQLLSMLPIE VEQIPERFSY MIKEVAVKRY NRIGAEGMTS EAVDGRSNAY ELNDFKEYE AIIDNYFNAR TRTKKGRAVF F

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.26 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13411
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
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