[English] 日本語
Yorodumi
- EMDB-69297: Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-69297
TitleCryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the TS-cleaving state
Map data
Sample
  • Complex: UnCas12m4a-crRNA-target DNA (TS-cleaving state)
    • Complex: crRNA-target DNA
      • Complex: crRNA
        • RNA: RNA (56-MER)
      • Complex: target DNA
        • DNA: DNA (39-MER)
        • DNA: DNA (39-MER)
      • Protein or peptide: UnCas12m4a
    • Complex: UnCas12m4a
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordsnuclease / DNA BINDING PROTEIN
Biological speciesLachnospiraceae bacterium ND2006 (bacteria) / bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsMorinaga H / Omura SN / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Intact RuvC catalytic site and bipartite ssDNA kinking are required for Cas12m nuclease activation
Authors: Morinaga H / Omura SN / Alfonse L / Ornstein A / Kobayashi TA / Onishi K / Makarova KS / Shmakov SA / Munoz G / Garrity AJ / DiTommaso T / Koonin EV / Maben Z / Nureki O
History
DepositionFeb 21, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_69297.png

Downloads & links

-
Map

FileDownload / File: emd_69297.map.gz / Format: CCP4 / Size: 11.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 146 pix.
= 136.327 Å		0.93 Å/pix.
x 146 pix.
= 136.327 Å		0.93 Å/pix.
x 146 pix.
= 136.327 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.39920607 - 0.6888198
Average (Standard dev.)0.0032759742 (±0.027029352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin878787
Dimensions146146146
Spacing146146146
CellA=B=C: 136.3275 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_69297_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_69297_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_69297_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : UnCas12m4a-crRNA-target DNA (TS-cleaving state)

EntireName: UnCas12m4a-crRNA-target DNA (TS-cleaving state)
Components
  • Complex: UnCas12m4a-crRNA-target DNA (TS-cleaving state)
    • Complex: crRNA-target DNA
      • Complex: crRNA
        • RNA: RNA (56-MER)
      • Complex: target DNA
        • DNA: DNA (39-MER)
        • DNA: DNA (39-MER)
      • Protein or peptide: UnCas12m4a
    • Complex: UnCas12m4a
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: UnCas12m4a-crRNA-target DNA (TS-cleaving state)

SupramoleculeName: UnCas12m4a-crRNA-target DNA (TS-cleaving state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)

+
Supramolecule #2: crRNA-target DNA

SupramoleculeName: crRNA-target DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3

+
Supramolecule #3: UnCas12m4a

SupramoleculeName: UnCas12m4a / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

+
Supramolecule #4: crRNA

SupramoleculeName: crRNA / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2

+
Supramolecule #5: target DNA

SupramoleculeName: target DNA / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #3-#4

+
Macromolecule #1: UnCas12m4a

MacromoleculeName: UnCas12m4a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 71.029164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG MAVEERTKKG VSVRVYKYGL VPKGCLPDEA KDELLRANNL WNKLVEISRK NQSDFDEVRK KAHPPYGEEM VRLETINEK IDDAYDRKRD ARKEAGTRDE THPLIIKANA VIEILKEERS EIYDTLKLLR TEADKSVDKK ALNESFKSNI K LARRETSL ...String:
MGHHHHHHGG MAVEERTKKG VSVRVYKYGL VPKGCLPDEA KDELLRANNL WNKLVEISRK NQSDFDEVRK KAHPPYGEEM VRLETINEK IDDAYDRKRD ARKEAGTRDE THPLIIKANA VIEILKEERS EIYDTLKLLR TEADKSVDKK ALNESFKSNI K LARRETSL NSDTKEEIIR NDFRTARDRT FKTGGRLRFH TFDGTGYWHF RFRRNDEKGK KVDDYTIDDL FAGEKPSPKK PL PNRFKFL SRDDTRRKPR LRLRTTLAGG RTNASKVFQE FDVIYHRPVP EGAIIPNAKI LRTRTGDKFR YDLVLTVYLP EPK HKDIPL DDAIGIDLGF REDPDDKYRK QVGAIISLDP SDEVEEIFAP PKMVKAFGHI DELKSVLDES AADLGMKIKP LMKD IRLPE DNEKYKQEYK LWNSIVNARA NVTLSFEKAY KLALWCKKKD AGIPEDITGP VVYWWKGYSR RYRELHNLRK KQLLN RKDF YRQIASRLVL RGLLIGVENF NLSKIARSKD EDNVLNNKAR ANRFLLSPSE FRAAIKNAAD REGIPCLEVN PANTSK ICF DCGTLNKNLG SEKNWVCPAC GCVHDRDTNA ARNIAKRALE KYLEDRKSAG K

+
Macromolecule #2: RNA (56-MER)

MacromoleculeName: RNA (56-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 18.057773 KDa
SequenceString:
GGAUAACGAC CCUGCGAAGU GGGGAGUAAC UUCGACGUAA AUUAGCUGCG CUUCAC

+
Macromolecule #3: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 12.21532 KDa
SequenceString:
(DT)(DG)(DA)(DA)(PST)(SC)(GS)(PST)(PST)(GS) (PST)(GS)(DA)(DA)(DG)(DC)(DG)(DC)(DA) (DG)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA)(DC) (DC)(DG)(DG)(DT)(DT)(DA)(DG)(DA)(DA)(DA)

+
Macromolecule #4: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: bacterium (bacteria)
Molecular weightTheoretical: 11.847616 KDa
SequenceString:
(DT)(DT)(DT)(DC)(DT)(DA)(DA)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DG)(DA)(DT)(DT)(DC)(DA)

+
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 108567
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