[English] 日本語
Yorodumi
- EMDB-28244: CryoEM characterization of BrxL -- a unique AAA+ phage restrictio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28244
TitleCryoEM characterization of BrxL -- a unique AAA+ phage restriction Factor.
Map datacombined 1.12 pixel data collected at Hutch with 1.16 pixel data from UW, ie down sampled from 1.12 to 1.16
Sample
  • Complex: dimer of heptamer complex of BrxL
    • Protein or peptide: Protease Lon-related BREX system protein BrxL
Keywordsphage restriction factor / AAA+ protein. BrxL / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding
Similarity search - Function
Lon-like protease BrxL / Lon-like protease BrxL-like / BREX system Lon protease-like BrxL, N-terminal / Lon-like protease BrxL-like, ATPase domain / BREX system Lon protease-like protein BrxL N-terminal / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protease Lon-related BREX system protein BrxL
Similarity search - Component
Biological speciesAcinetobacter (bacteria) / Acinetobacter sp. NEB 394 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShen BW / Stoddard BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105691 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor.
Authors: Betty W Shen / Lindsey A Doyle / Rachel Werther / Abigail A Westburg / Daniel P Bies / Stephanie I Walter / Yvette A Luyten / Richard D Morgan / Barry L Stoddard / Brett K Kaiser /
Abstract: Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been ...Bacteriophage exclusion ('BREX') systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.
History
DepositionSep 27, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28244.png

Downloads & links

-
Map

FileDownload / File: emd_28244.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcombined 1.12 pixel data collected at Hutch with 1.16 pixel data from UW, ie down sampled from 1.12 to 1.16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 392 pix.
= 454.72 Å		1.16 Å/pix.
x 392 pix.
= 454.72 Å		1.16 Å/pix.
x 392 pix.
= 454.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.17271502 - 0.78393894
Average (Standard dev.)0.0008664412 (±0.030259999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 454.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A

Fileemd_28244_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_28244_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : dimer of heptamer complex of BrxL

EntireName: dimer of heptamer complex of BrxL
Components
  • Complex: dimer of heptamer complex of BrxL
    • Protein or peptide: Protease Lon-related BREX system protein BrxL

-
Supramolecule #1: dimer of heptamer complex of BrxL

SupramoleculeName: dimer of heptamer complex of BrxL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter (bacteria)
Molecular weightTheoretical: 1.05 MDa

-
Macromolecule #1: Protease Lon-related BREX system protein BrxL

MacromoleculeName: Protease Lon-related BREX system protein BrxL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter sp. NEB 394 (bacteria)
Molecular weightTheoretical: 75.703539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESANDKELD QLLNEHFAGR VVRKDLTKLI KEGANVPVYV LEYLLGMYCA SDDPEIIEQG LRNVKTVLAE NYVRPDEAEK VKSLVRERG SYKVIDRVTV KLNERKDKYE ASFSNLGIKD AEISAGIVKE YEKLLVGGIW VIATLSYYFE EGQTSSPFGV S LLKPIQMP ...String:
MESANDKELD QLLNEHFAGR VVRKDLTKLI KEGANVPVYV LEYLLGMYCA SDDPEIIEQG LRNVKTVLAE NYVRPDEAEK VKSLVRERG SYKVIDRVTV KLNERKDKYE ASFSNLGIKD AEISAGIVKE YEKLLVGGIW VIATLSYYFE EGQTSSPFGV S LLKPIQMP NMNMDELFSG RAALSTDQWR ESLIRSIGME PASLKEDVQW HLLARMVPFV ENNYNVCELG PRGTGKSHIY KE CSPNSIL VSGGQTTVAN LFYNMSSRRI GLVGLWDVVA FDEVAGISFK DKDGVQIMKD YMASGSFARG REQMEASASM VFV GNINQS VESLVKTSHL LAPFPEAMID SAFFDRFHAY IPGWEIPKMR PEFFTNRYGL IVDYLAEFFR EMRKRSFADS IEKY FKLGN NLNQRDVIAV RKTVSGLMKL LYPHGQFNKE DVRQCLEYAL QVRRRVKEQL KKIGGMEFYD VHFSYIDNDT LEEHF VSVK EQGGGGLIPE GPAKPGFLYT IGLSNKGMPG LYRLELQVTK GSGKLATSGL WNSSSAKEQV KIAFDYFKAN ASRISG GSK VMEHDFHLHV VELQNTGPLS HLALPSLVAF ASGLLGRSVQ SQMVVLGDMS LGGSVTPVES IAECLQVAFD AGAKKVA LP MSSAADIPTI PVELFTKFQT SFYADPVDAV FKGLGVD

UniProtKB: Protease Lon-related BREX system protein BrxL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 8 / Details: 20 mM TrisHCl, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was mono-dispersed

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 3000 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Details: 2980 movies at 1.12 pixel was extracted at box size of 406 pix, fourier cropped to box size of 392 pix and combined with 100 movies collected at 1.16 pix size
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 38000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 96079
Startup modelType of model: NONE
Final reconstructionNumber classes used: 93 / Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 89373
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. 3.3.2)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8emc:
CryoEM characterization of BrxL -- a unique AAA+ phage restriction Factor.

+
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