[English] 日本語
Yorodumi
- EMDB-66405: PmCas12m-crRNA-target DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66405
TitlePmCas12m-crRNA-target DNA complex
Map data
Sample
  • Complex: Pmcas12m
    • Protein or peptide: Transposase
    • RNA: RNA
    • DNA: DNA(TS)
    • DNA: DNA(NTS)
  • Ligand: MAGNESIUM ION
Keywordscrispr / DNA / RNA / cyro-EM / Complex / DNA BINDING PROTEIN/RNA/DNA / DNA BINDING PROTEIN-RNA-DNA complex
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPelomicrobium methylotrophicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMeng J / Tao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171212 China
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing.
Authors: Tao Yu / Meng Ji / Donglin Yu / Zhao Guan / Rongyi Zhu / Yunpeng Jiang / Zhiyi Yang / Lizhen Qiu / Ziyi Zhang / Jiawei Mu / Fengbiao Mao / Kuanhui Xiang / Lin Bai / Kailong Li /
Abstract: CRISPR-based epigenome editing represents a programmable strategy to precisely modulate gene expression, holding promise for therapeutic applications. However, the large size of dCas proteins ...CRISPR-based epigenome editing represents a programmable strategy to precisely modulate gene expression, holding promise for therapeutic applications. However, the large size of dCas proteins substantially impedes delivery using adeno-associated virus (AAV) vectors. Here, through iterative bioinformatics analysis, structure-guided predictions and functional assays, we identified and characterized a miniature subtype V-M CRISPR-Cas12m from Pelomicrobium methylotrophicum. PmCas12m exhibited flexible 5'-YTN-3' PAM-dependent recognition and robust double-stranded DNA-binding properties while lacking DNA cleavage activity, thus rendering it a valuable tool for epigenome editing. Cryo-electron microscopy structures of PmCas12m unveiled its molecular mechanism of target DNA binding. Guided by these structural insights, we used deep mutational scanning and protein engineering to develop xCas12m, a hypercompact variant with highly potent and specific epigenome-editing capabilities in human cells. We further constructed the xCas12m-CRISPRoff platform in a single AAV vector, which achieved durable epigenetic silencing and effective inhibition of hepatitis B virus infection in a mouse model. Collectively, these findings establish xCas12m as a versatile epigenome-editing platform with notable potential for treating diseases, paving the way for clinical translation of epigenetic therapies.
History
DepositionSep 29, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66405.png

Downloads & links

-
Map

FileDownload / File: emd_66405.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 256 pix.
= 378.88 Å		1.48 Å/pix.
x 256 pix.
= 378.88 Å		1.48 Å/pix.
x 256 pix.
= 378.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.374078 - 2.2820768
Average (Standard dev.)-0.00021350938 (±0.033214614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 378.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66405_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66405_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pmcas12m

EntireName: Pmcas12m
Components
  • Complex: Pmcas12m
    • Protein or peptide: Transposase
    • RNA: RNA
    • DNA: DNA(TS)
    • DNA: DNA(NTS)
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Pmcas12m

SupramoleculeName: Pmcas12m / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: protein
Source (natural)Organism: Pelomicrobium methylotrophicum (bacteria)

-
Macromolecule #1: Transposase

MacromoleculeName: Transposase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pelomicrobium methylotrophicum (bacteria)
Molecular weightTheoretical: 67.672914 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKNIAVQTNK AATESAVTVF RYGLLAPINW GRDVEDELYR MNALWNKLVE IERANRERYR EIISTSPALS EVSERIEALH REREDLIAE RKRRRASARS KSKADTADLD ERIKAIKAEL APLYEQRKSL AAEAREQQKP LLDALEAERR EAVKAARQSS G CFWPNYNA ...String:
MKNIAVQTNK AATESAVTVF RYGLLAPINW GRDVEDELYR MNALWNKLVE IERANRERYR EIISTSPALS EVSERIEALH REREDLIAE RKRRRASARS KSKADTADLD ERIKAIKAEL APLYEQRKSL AAEAREQQKP LLDALEAERR EAVKAARQSS G CFWPNYNA VIASYEIARK RAMKTGADLR FRRFSREGRL VNQIQGGMSV EDLFSCRHSQ VGIRLGGQSR GRQTGTLYVT AY TGRDESG RRIRRNVEFP IILHRPFPKD AVIKEVAVNI RRRSPSVVSG QTETDDGRII EYGEAEYSVA FTCQTPAPEK SAG SSAAGI NIGWKRVSGG LRVATAAFHD GTFEHLILPD EWVKKYERVQ ALRSGIDDAD NEMHAALRQA LQGMPLWERD GPMV EGLSD SDHRLLSAIK RAPRAPGRAM DALAWRLKET PNMPFVADLG ATIEAWRKAR KRMILEMDNL RGKLLARRKD LYRTF AARI AAYAGAIAID DTDYRQAALV ERTDGEDLEL HEQARRQRVM AAPYELRLAI EQAAAKRGGY VERHRGSVNH CRACRS RNV SGDIARHCHA CGAVFDVDEN AALNLLHTLI AGPARAVE

UniProtKB: Uncharacterized protein

-
Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Pelomicrobium methylotrophicum (bacteria)
Molecular weightTheoretical: 17.993723 KDa
SequenceString:
AUCACAAAGC CUGCUCCGCG GCUUGGUAGU GGAGACCUCC CUAUCAGUGA UAGAGA

-
Macromolecule #3: DNA(TS)

MacromoleculeName: DNA(TS) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pelomicrobium methylotrophicum (bacteria)
Molecular weightTheoretical: 11.091149 KDa
SequenceString:
(DA)(DT)(DA)(DC)(DG)(DT)(DT)(DC)(DT)(DC) (DT)(DA)(DT)(DC)(DA)(DC)(DT)(DG)(DA)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DA)(DG)(DT)(DC)(DT)(DG)(DC)

-
Macromolecule #4: DNA(NTS)

MacromoleculeName: DNA(NTS) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pelomicrobium methylotrophicum (bacteria)
Molecular weightTheoretical: 11.060139 KDa
SequenceString:
(DG)(DC)(DA)(DG)(DA)(DC)(DT)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DT)(DC)(DA) (DG)(DT)(DG)(DA)(DT)(DA)(DG)(DA)(DG) (DA)(DA)(DC)(DG)(DT)(DA)(DT)

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: METHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 155865
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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