[English] 日本語
Yorodumi
- EMDB-34824: Cryo-EM structure of the Cas12m2-crRNA binary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34824
TitleCryo-EM structure of the Cas12m2-crRNA binary complex
Map data
Sample
  • Complex: Cas12m2-crRNA
    • Complex: crRNA
      • RNA: RNA (56-MER)
    • Complex: Cas12m2
      • Protein or peptide: Cas12m2
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsCRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN
Biological speciesMycolicibacterium mucogenicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsOmura NS / Nakagawa R / Wu YW / Sudfeld C / Warren VR / Hirano H / Kusakizako T / Kise Y / Lebbink HGJ / Itoh Y ...Omura NS / Nakagawa R / Wu YW / Sudfeld C / Warren VR / Hirano H / Kusakizako T / Kise Y / Lebbink HGJ / Itoh Y / Oost VDJ / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Authors: Satoshi N Omura / Ryoya Nakagawa / Christian Südfeld / Ricardo Villegas Warren / Wen Y Wu / Hisato Hirano / Charlie Laffeber / Tsukasa Kusakizako / Yoshiaki Kise / Joyce H G Lebbink / ...Authors: Satoshi N Omura / Ryoya Nakagawa / Christian Südfeld / Ricardo Villegas Warren / Wen Y Wu / Hisato Hirano / Charlie Laffeber / Tsukasa Kusakizako / Yoshiaki Kise / Joyce H G Lebbink / Yuzuru Itoh / John van der Oost / Osamu Nureki /
Abstract: RNA-guided type V CRISPR-Cas12 effectors provide adaptive immunity against mobile genetic elements (MGEs) in bacteria and archaea. Among diverse Cas12 enzymes, the recently identified Cas12m2 (CRISPR- ...RNA-guided type V CRISPR-Cas12 effectors provide adaptive immunity against mobile genetic elements (MGEs) in bacteria and archaea. Among diverse Cas12 enzymes, the recently identified Cas12m2 (CRISPR-Cas type V-M) is highly compact and has a unique RuvC active site. Although the non-canonical RuvC triad does not permit dsDNA cleavage, Cas12m2 still protects against invading MGEs through transcriptional silencing by strong DNA binding. However, the molecular mechanism of RNA-guided genome inactivation by Cas12m2 remains unknown. Here we report cryo-electron microscopy structures of two states of Cas12m2-CRISPR RNA (crRNA)-target DNA ternary complexes and the Cas12m2-crRNA binary complex, revealing structural dynamics during crRNA-target DNA heteroduplex formation. The structures indicate that the non-target DNA strand is tightly bound to a unique arginine-rich cluster in the recognition (REC) domains and the non-canonical active site in the RuvC domain, ensuring strong DNA-binding affinity of Cas12m2. Furthermore, a structural comparison of Cas12m2 with TnpB, a putative ancestor of Cas12 enzymes, suggests that the interaction of the characteristic coiled-coil REC2 insertion with the protospacer-adjacent motif-distal region of the heteroduplex is crucial for Cas12m2 to engage in adaptive immunity. Collectively, our findings improve mechanistic understanding of diverse type V CRISPR-Cas effectors and provide insights into the evolution of TnpB to Cas12 enzymes.
History
DepositionNov 21, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34824.png

Downloads & links

-
Map

FileDownload / File: emd_34824.map.gz / Format: CCP4 / Size: 3.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4229 Å
Density
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.2826083 - 4.095807
Average (Standard dev.)0.011523184 (±0.21054934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin291625
Dimensions9210496
Spacing1049296
CellA: 147.9816 Å / B: 130.9068 Å / C: 136.59839 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34824_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34824_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34824_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cas12m2-crRNA

EntireName: Cas12m2-crRNA
Components
  • Complex: Cas12m2-crRNA
    • Complex: crRNA
      • RNA: RNA (56-MER)
    • Complex: Cas12m2
      • Protein or peptide: Cas12m2
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

-
Supramolecule #1: Cas12m2-crRNA

SupramoleculeName: Cas12m2-crRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium mucogenicum (bacteria)

-
Supramolecule #2: crRNA

SupramoleculeName: crRNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

-
Supramolecule #3: Cas12m2

SupramoleculeName: Cas12m2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Macromolecule #1: RNA (56-MER)

MacromoleculeName: RNA (56-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Mycolicibacterium mucogenicum (bacteria)
Molecular weightTheoretical: 18.277932 KDa
SequenceString:
GUGUCAUAGC CCAGCUUGGC GGGCGAAGGC CAAGACGGAG AUGAGGUGCG CGUGGC

-
Macromolecule #2: Cas12m2

MacromoleculeName: Cas12m2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium mucogenicum (bacteria)
Molecular weightTheoretical: 66.342883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTMTVHTMG VHYKWQIPEV LRQQLWLAHN LREDLVSLQL AYDDDLKAIW SSYPDVAQAE DTMAAAEADA VALSERVKQA RIEARSKKI STELTQQLRD AKKRLKDARQ ARRDAIAVVK DDAAERRKAR SDQLAADQKA LYGQYCRDGD LYWASFNTVL D HHKTAVKR ...String:
MTTMTVHTMG VHYKWQIPEV LRQQLWLAHN LREDLVSLQL AYDDDLKAIW SSYPDVAQAE DTMAAAEADA VALSERVKQA RIEARSKKI STELTQQLRD AKKRLKDARQ ARRDAIAVVK DDAAERRKAR SDQLAADQKA LYGQYCRDGD LYWASFNTVL D HHKTAVKR IAAQRASGKP ATLRHHRFDG SGTIAVQLQR QAGAPPRTPM VLADEAGKYR NVLHIPGWTD PDVWEQMTRS QC RQSGRVT VRMRCGSTDG QPQWIDLPVQ VHRWLPADAD ITGAELVVTR VAGIYRAKLC VTARIGDTEP VTSGPTVALH LGW RSTEEG TAVATWRSDA PLDIPFGLRT VMRVDAAGTS GIIVVPATIE RRLTRTENIA SSRSLALDAL RDKVVGWLSD NDAP TYRDA PLEAATVKQW KSPQRFASLA HAWKDNGTEI SDILWAWFSL DRKQWAQQEN GRRKALGHRD DLYRQIAAVI SDQAG HVLV DDTSVAELSA RAMERTELPT EVQQKIDRRR DHAAPGGLRA SVVAAMTRDG VPVTIVAAAD FTRTHSRCGH VNPADD RYL SNPVRCDGCG AMYDQDRSFV TLMLRAATAP SNP

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115501
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