[English] 日本語
Yorodumi
- EMDB-38204: Cryo-EM structure of an anti-phage defense complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38204
TitleCryo-EM structure of an anti-phage defense complex
Map data
Sample
  • Complex: DUF4297-HerA
    • Protein or peptide: ATP-binding protein
    • Protein or peptide: DUF4297
KeywordsDUF4297-HerA / Nuclease / Helicase / DNA BINDING PROTEIN
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsWang Y / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2024
Title: Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex.
Authors: Qiyin An / Yong Wang / Zhenhua Tian / Jie Han / Jinyue Li / Fumeng Liao / Feiyang Yu / Haiyan Zhao / Yancheng Wen / Heng Zhang / Zengqin Deng /
Abstract: Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in ...Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297-HerA, demonstrating that DUF4297-HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.
History
DepositionDec 5, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38204.png

Downloads & links

-
Map

FileDownload / File: emd_38204.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-1.2026427 - 1.9705122
Average (Standard dev.)0.002745965 (±0.06503139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_38204_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38204_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DUF4297-HerA

EntireName: DUF4297-HerA
Components
  • Complex: DUF4297-HerA
    • Protein or peptide: ATP-binding protein
    • Protein or peptide: DUF4297

-
Supramolecule #1: DUF4297-HerA

SupramoleculeName: DUF4297-HerA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: ATP-binding protein

MacromoleculeName: ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.870047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA ...String:
MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA VDEKQEGYKG LNNSHIIIFD IHSEYENAFP NSNVLNVDTL TLPYWLLNGD ELEELFLDTE ANDHNQRNVF RQ AITLNKK IHFQGDPATK EIISFHSPYY FDINEVINYI NNRNNERKNK DNEHIWSDEE GNFKFDNENA HRLFKENVTP DGS SAGALN GKLLNFVDRL QSKIFDKRLD FILGEGSKSV TFKETLETLI SYGKDKSNIT ILDVSGVPFE VLSICVSLIS RLIF EFGYH SKKIKRKSNE NQDIPILIVY EEAHKYAPKS DLSKYRTSKE AIERIAKEGR KYGVTLLLAS QRPSEISETI FSQCN TFIS MRLTNPDDQN YVKRLLPDTV GDITNLLPSL KEGEALIMGD SISIPSIVKI EKCTIPPSSI DIKYLDEWRK EWVDSE FDK IIEQWSKS

UniProtKB: UNIPROTKB: A0A9X9SUP5

-
Macromolecule #2: DUF4297

MacromoleculeName: DUF4297 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.971949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF ...String:
MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF QCEDYEAEHY LYSNAFRKTY DISCNKKDRR IKKSDFVESI NKSKVLFNIW FYQYEGRKEY LRKLKESFIR RS VNTSPYA RFFILEFQDK TDIKTVKDCI YKIQSNWSNL SKRTDRPYSP FLLFHGTSDA NLYELKNQLF NEDLIFTDGY PFK GSVFTP KMLIEGFSNK EIHFQFINDI DDFNETLNSI NIRKEVYQFY TENCLDIPSQ LPQVNIQVKD FADIKEIV

UniProtKB: UNIPROTKB: A0A9X9SUN3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290611
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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://pdbjlvh1.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