[English] 日本語
Yorodumi
- EMDB-43560: Cryo-EM structure of a type II ZorAB complex from Sulfuricurvum k... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43560
TitleCryo-EM structure of a type II ZorAB complex from Sulfuricurvum kujiense
Map datasharpened map used for model refinements
Sample
  • Complex: ZorAB complex
    • Protein or peptide: MotA/TolQ/ExbB proton channel domain-containing protein
    • Protein or peptide: Motility protein B-like N-terminal domain-containing protein
Keywordsphage defense / zorya / phage / membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane / plasma membrane
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
MotA/TolQ/ExbB proton channel domain-containing protein / OmpA-like domain-containing protein
Similarity search - Component
Biological speciesSulfuricurvum kujiense DSM 16994 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Commun / Year: 2025
Title: Modularity of Zorya defense systems during phage inhibition.
Authors: Giuseppina Mariano / Justin C Deme / Jennifer J Readshaw / Matthew J Grobbelaar / Mackenzie Keenan / Yasmin El-Masri / Lindsay Bamford / Suraj Songra / Tim R Blower / Tracy Palmer / Susan M Lea /
Abstract: Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. ...Bacteria have evolved an extraordinary diversity of defense systems against bacteriophage (phage) predation. However, the molecular mechanisms underlying these anti-phage systems often remain elusive. Here, we provide mechanistic and structural insights into Zorya phage defense systems. Using cryo-EM structural analyses, we show that the Zorya type I and II core components, ZorA and ZorB, assemble in a 5:2 complex that is similar to inner-membrane ion-driven, rotary motors that power flagellar rotation, type 9 secretion, gliding and the Ton nutrient uptake systems. The ZorAB complex has an elongated cytoplasmic tail assembled by bundling the C-termini of the five ZorA subunits. Mutagenesis demonstrates that peptidoglycan binding by the periplasmic domains of ZorB, the structured cytoplasmic tail of ZorA, and ion flow through the motor is important for function in both type I and II systems. Furthermore, we identify ZorE as the effector module of the Zorya II system, possessing nickase activity. Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system.
History
DepositionJan 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43560.png

Downloads & links

-
Map

FileDownload / File: emd_43560.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map used for model refinements
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å		0.72 Å/pix.
x 480 pix.
= 347.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.5800436 - 5.8315945
Average (Standard dev.)0.0004014004 (±0.065064296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 347.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43560_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map

Fileemd_43560_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_43560_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_43560_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ZorAB complex

EntireName: ZorAB complex
Components
  • Complex: ZorAB complex
    • Protein or peptide: MotA/TolQ/ExbB proton channel domain-containing protein
    • Protein or peptide: Motility protein B-like N-terminal domain-containing protein

-
Supramolecule #1: ZorAB complex

SupramoleculeName: ZorAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfuricurvum kujiense DSM 16994 (bacteria)

-
Macromolecule #1: MotA/TolQ/ExbB proton channel domain-containing protein

MacromoleculeName: MotA/TolQ/ExbB proton channel domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sulfuricurvum kujiense DSM 16994 (bacteria)
Molecular weightTheoretical: 42.445297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIHNMAYFGV GLITLMFLIF VMNRRNKSIQ ELAPGILITT GIFFTFVGIA IGLVHFNADN VDDSLPTLLN GIKTAFWASA TGVFFALII KILDIFDLTR TNESSAVEGM SIDDIVTYQA KQTDVLVEIL RSIKNMHSSI AAQDDSSLVS QIALLRDDSN K KSDALRQE ...String:
MIHNMAYFGV GLITLMFLIF VMNRRNKSIQ ELAPGILITT GIFFTFVGIA IGLVHFNADN VDDSLPTLLN GIKTAFWASA TGVFFALII KILDIFDLTR TNESSAVEGM SIDDIVTYQA KQTDVLVEIL RSIKNMHSSI AAQDDSSLVS QIALLRDDSN K KSDALRQE FRDFAATMAE NNSKIFIEAL KDVIKNFNDK ISEQFGDNFK QLNQAVEKTV IWQENYRNQM AQSIETMTLI AS MLESQAH DYSIIVSNSA EFESHVSAMG RSLEEITFQR EQLQSMIHSL VNFLESASDS LPLIGQKVDD MTERLVKGMN EAT EEVQKQ VTILDHELEI ALKRSLEGLG QQLASLSNKF VQDYTPLTEK LREVVALAAK QR

UniProtKB: MotA/TolQ/ExbB proton channel domain-containing protein

-
Macromolecule #2: Motility protein B-like N-terminal domain-containing protein

MacromoleculeName: Motility protein B-like N-terminal domain-containing protein
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sulfuricurvum kujiense DSM 16994 (bacteria)
Molecular weightTheoretical: 31.944371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSLPQKKHH HKEDYWISLS DMMTSLMMLF LLISVIYMIK VQDSVKVPQI YKETTQGLNH ALKKEFDKDL MKWGAVIDKD LTVRFQQPD ILFATGSSAL TPRFKEILDD FFIRYLKIMM SKPFINNIEE IRIEGHTSSM WEGESDRGKA YFKNMTLSQE R TRATLEYI ...String:
MSSLPQKKHH HKEDYWISLS DMMTSLMMLF LLISVIYMIK VQDSVKVPQI YKETTQGLNH ALKKEFDKDL MKWGAVIDKD LTVRFQQPD ILFATGSSAL TPRFKEILDD FFIRYLKIMM SKPFINNIEE IRIEGHTSSM WEGESDRGKA YFKNMTLSQE R TRATLEYI MTSDKINLTG EQKEWLMRHF SAIGFSSGHP LTNKGTYLVD GESEDSQLSQ RVEFRVRTNI ERKVADIVEK EN LYFQGQF GSWSHPQFEK GGGSGGGSGG GSWSHPQFEK

UniProtKB: OmpA-like domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 57.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 366883
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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