[English] 日本語
Yorodumi
- EMDB-80302: Cryo-EM structure of TasH-tigRNA-MM5 dsDNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80302
TitleCryo-EM structure of TasH-tigRNA-MM5 dsDNA complex
Map data
Sample
  • Complex: Putative nuclease
    • Protein or peptide: Putative nuclease
    • RNA: RNA (37-MER)
    • DNA: DNA (38-MER)
    • DNA: DNA (38-MER)
KeywordsPutative nuclease / ANTIVAL PROTEIN/RNA/DNA / ANTIVAL PROTEIN-RNA-DNA complex
Biological speciesSalicola phage CGphi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhang H / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Molecular basis of single-mismatch-induced nuclease-to-nickase conversion in TIGR-TasH.
Authors: Ruimin Zhou / Yancheng Zhan / Yangyue Sun / Runqin Wang / Tongyao Wang / Zhikun Liu / Zhengda Shan / Xuzichao Li / Shuqin Zhang / Nan Sun / Heng Zhang / Zhiyong Yuan / Jie Yang /
Abstract: Tandem interspaced guide RNA (TIGR)-Tas systems are a distinct class of RNA-guided double-stranded DNA nucleases that employ dual-spacer guide RNAs (tigRNAs) for PAM-independent target recognition. A ...Tandem interspaced guide RNA (TIGR)-Tas systems are a distinct class of RNA-guided double-stranded DNA nucleases that employ dual-spacer guide RNAs (tigRNAs) for PAM-independent target recognition. A single mismatch between the tigRNA and target DNA can convert Salicola phage CGphi29 (Sp)TasH from a double-strand nuclease into a nickase in a position-dependent manner, but the molecular basis underlying this functional switch remains unknown. Here, we combined biochemical analyses and cryo-electron microscopy to investigate tigRNA maturation and mismatched target recognition by the Nop domain of SpTasH. We show that the Nop domain is required for pre-tigRNA processing and stabilizes the mature tigRNA through extensive interactions, thereby establishing a cleavage-competent ribonucleoprotein complex. Structural analyses of SpTasH complexes bound to substrates containing single mismatches reveal that a mismatch at the 5'-most position of spacer A is readily accommodated through Nop domain-mediated stabilization of the spacer-target heteroduplex. In contrast, a mismatch proximal to the cleavage site destabilizes the heteroduplex, preventing recruitment of the corresponding HNH domain, thereby converting the complex into a nickase. Together, these findings establish the structural basis for position-dependent mismatch recognition and reveal how Nop domain-mediated tigRNA-target stabilization enables differential responses to mismatches, providing a foundation for engineering TIGR-Tas systems for genome-editing applications.
History
DepositionApr 14, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_80302.png

Downloads & links

-
Map

FileDownload / File: emd_80302.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 300 pix.
= 207.6 Å		0.69 Å/pix.
x 300 pix.
= 207.6 Å		0.69 Å/pix.
x 300 pix.
= 207.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.31545323 - 0.57292026
Average (Standard dev.)-0.0007205107 (±0.019912424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 207.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_80302_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_80302_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Putative nuclease

EntireName: Putative nuclease
Components
  • Complex: Putative nuclease
    • Protein or peptide: Putative nuclease
    • RNA: RNA (37-MER)
    • DNA: DNA (38-MER)
    • DNA: DNA (38-MER)

-
Supramolecule #1: Putative nuclease

SupramoleculeName: Putative nuclease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salicola phage CGphi29 (virus)

-
Macromolecule #1: Putative nuclease

MacromoleculeName: Putative nuclease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salicola phage CGphi29 (virus)
Molecular weightTheoretical: 40.031242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKQVLKEQA SHCEITGAPL AGLPELVDVD RITERFQGGT YTPDNTRVLT PRAHMERHGI LRERDQWLEE LKAMMDDRAQ TMKVVMKMN NQLLAYQRQT DHARQSTEQF LQDTLDASNK RLAQIDREVT KHIKHAKDPL AQAAMGVPGV GPITVAGLQT Y VDLEKAKS ...String:
MNKQVLKEQA SHCEITGAPL AGLPELVDVD RITERFQGGT YTPDNTRVLT PRAHMERHGI LRERDQWLEE LKAMMDDRAQ TMKVVMKMN NQLLAYQRQT DHARQSTEQF LQDTLDASNK RLAQIDREVT KHIKHAKDPL AQAAMGVPGV GPITVAGLQT Y VDLEKAKS ASALWAYIGI DKPSHDRYTK GEAGGGNKTL RTMVWNMANS MIKNRKCPYR TVYEQTKERL AVSEKVTKSR NT QGQLIEC AWKDTKPSHR HGAALRAVMK HFLADYWFVG RELAGLDTRP LYVQEKLGHT GIVQPQERGW EWGGSWSHPQ FEK GGGSGG GSGGSAWSHP QFEKNLYFQS GSHHHHHH

-
Macromolecule #2: RNA (37-MER)

MacromoleculeName: RNA (37-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Salicola phage CGphi29 (virus)
Molecular weightTheoretical: 11.948239 KDa
SequenceString:
AGUCAUUCCG UUAAAGACAA CCACGGAGAC GAAGCGA

-
Macromolecule #3: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Salicola phage CGphi29 (virus)
Molecular weightTheoretical: 11.60645 KDa
SequenceString:
(DC)(DC)(DC)(DT)(DA)(DA)(DG)(DG)(DC)(DA) (DA)(DT)(DT)(DC)(DC)(DG)(DT)(DT)(DA)(DC) (DG)(DT)(DC)(DT)(DC)(DC)(DG)(DT)(DG) (DT)(DT)(DA)(DC)(DA)(DG)(DG)(DA)(DC)

-
Macromolecule #4: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Salicola phage CGphi29 (virus)
Molecular weightTheoretical: 11.784576 KDa
SequenceString:
(DG)(DT)(DC)(DC)(DT)(DG)(DT)(DA)(DA)(DC) (DA)(DC)(DG)(DG)(DA)(DG)(DA)(DC)(DG)(DT) (DA)(DA)(DC)(DG)(DG)(DA)(DA)(DT)(DT) (DG)(DC)(DC)(DT)(DT)(DA)(DG)(DG)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 315323
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
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