[English] 日本語
Yorodumi
- EMDB-49856: Engineered OrufIscB-omegaRNA-target DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49856
TitleEngineered OrufIscB-omegaRNA-target DNA complex
Map dataEngineered OrufIscB-omegaRNA-target DNA complex
Sample
  • Complex: Engineered OrufIscB-omegaRNA-target DNA complex
    • DNA: NTS
    • Protein or peptide: OrufIscB-REC-swap 49
    • DNA: DNA TS
    • RNA: RNA (162-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsGene editing / IscB / OMEGA / RNA-guided nuclease / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesmetagenome (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsXu P / Zhu S / Zhang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Biotechnol / Year: 2025
Title: Evolution-guided protein design of IscB for persistent epigenome editing in vivo.
Authors: Soumya Kannan / Han Altae-Tran / Shiyou Zhu / Peiyu Xu / Daniel Strebinger / Rachel Oshiro / Guilhem Faure / Lukas Moeller / Julie Pham / Kepler S Mears / Heyuan M Ni / Rhiannon K Macrae / Feng Zhang /
Abstract: Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is ...Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is difficult to engineer variants with enhanced activity while maintaining specificity. Here we engineer the compact Obligate Mobile Element Guided Activity (OMEGA) RNA-guided endonuclease IscB and its guiding RNA (ωRNA) by combining ortholog screening, structure-guided protein domain design and RNA engineering, and deep learning-based structure prediction to generate an improved variant, NovaIscB. We show that the compact NovaIscB achieves up to 40% indel activity (~100-fold improvement over wild-type OgeuIscB) on the human genome with improved specificity relative to existing IscBs. We further show that NovaIscB can be fused with a methyltransferase to create a programmable transcriptional repressor, OMEGAoff, that is compact enough to be packaged in a single adeno-associated virus vector for persistent in vivo gene repression. This study highlights the power of combining natural diversity with protein engineering to design enhanced enzymes for molecular biology applications.
History
DepositionMar 21, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49856.png

Downloads & links

-
Map

FileDownload / File: emd_49856.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEngineered OrufIscB-omegaRNA-target DNA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.058891054 - 2.1395812
Average (Standard dev.)0.0011762189 (±0.02406652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional Map 2

Fileemd_49856_additional_1.map
AnnotationAdditional Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional Map 1

Fileemd_49856_additional_2.map
AnnotationAdditional Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_49856_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_49856_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Engineered OrufIscB-omegaRNA-target DNA complex

EntireName: Engineered OrufIscB-omegaRNA-target DNA complex
Components
  • Complex: Engineered OrufIscB-omegaRNA-target DNA complex
    • DNA: NTS
    • Protein or peptide: OrufIscB-REC-swap 49
    • DNA: DNA TS
    • RNA: RNA (162-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

-
Supramolecule #1: Engineered OrufIscB-omegaRNA-target DNA complex

SupramoleculeName: Engineered OrufIscB-omegaRNA-target DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: metagenome (others)

-
Macromolecule #1: NTS

MacromoleculeName: NTS / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.885773 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DT)(DG)(DA)(DC)(DT)(DT) (DC)(DT)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DT) (DT)(DC)(DC)(DC)(DG)(DG)(DG)(DT)(DA)

-
Macromolecule #3: DNA TS

MacromoleculeName: DNA TS / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.030771 KDa
SequenceString:
(DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DA)(DA) (DT)(DT)(DT)(DT)(DA)(DT)(DG)(DA)(DG)(DA) (DA)(DG)(DT)(DC)(DA)(DT)(DT)(DT)(DA) (DA)(DT)(DA)(DA)(DG)(DG)(DC)(DC)(DA)(DC)

-
Macromolecule #2: OrufIscB-REC-swap 49

MacromoleculeName: OrufIscB-REC-swap 49 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 69.258656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RYVYVLDVDG KPLMPTCRFG KVRRMLKSGQ AKAVDTLPFT IQLTYKPRTR ILQPVTLGQD PGRTNIGMAA VRFDGKELGR FHCITRNKE IPKLMADRMA ARKASRRGER LARKRLARKL HTTAKHLNGR ILPGCSEPIA VKDIINTESR FNNRILTKCK V CGKNTPLR ...String:
RYVYVLDVDG KPLMPTCRFG KVRRMLKSGQ AKAVDTLPFT IQLTYKPRTR ILQPVTLGQD PGRTNIGMAA VRFDGKELGR FHCITRNKE IPKLMADRMA ARKASRRGER LARKRLARKL HTTAKHLNGR ILPGCSEPIA VKDIINTESR FNNRILTKCK V CGKNTPLR RNVRELLLEN IVRFLPLESE LKETLKRTIL EGQQGNINKL FRKLRKVYKI TLNQKDWPGK NLTDIAKNKL PG RLPFCKE HFAENEKFTT IEKSTFRLTP TATQLLRTHI NLFRKLSGIL PVTDVAVELN KFAFMQLDNP EMKKREIDFC HGP LCGTGG LEAAVKEQQD GKCLLCGKES IGHYHHIVPR SRRGSNTIAN IAGLCPKCHE LVHKDADTAE SLTEMKTGLM KKYG GTSVL NQIIPKLVET LADLFPGHFH VTNGWNTKEF REKHHLEKDH DVDAYCIACS HLKPEETLVE TEPFEILQFR KHNRA IIHH QTERTYKLDG VTVAKNRKKR MEQKTDSLED WYVDMAKEHG KTQADAMRSR LTVIKSTRYY NTPGRMMPGT VFLYEG KRY VMTGQITNGK YYRAYGQEKR NFPAVKVRIL TKNTGLVFVA

-
Macromolecule #4: RNA (162-MER)

MacromoleculeName: RNA (162-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 73.060102 KDa
SequenceString: GGGCCUUAUU AAAUGACUUC UCGUCAAUAA CCCAUGACUG AAGUCAUGGG CUUGCAGAUG CAGGUCCUGA UGGAAGAAAG GGUUACUGA GCAGAGCAGU GACAUGUCAU UCGCCGCGGG GUGAUUCCAA GCUCCGCGCU CCGGCUAGAC AUGCCCAUGC U UUGGAAAC ...String:
GGGCCUUAUU AAAUGACUUC UCGUCAAUAA CCCAUGACUG AAGUCAUGGG CUUGCAGAUG CAGGUCCUGA UGGAAGAAAG GGUUACUGA GCAGAGCAGU GACAUGUCAU UCGCCGCGGG GUGAUUCCAA GCUCCGCGCU CCGGCUAGAC AUGCCCAUGC U UUGGAAAC UUUAACGGUA UGUGCGGUUU UCCGCUUAUA CCGGCUUACA ACAAAUAAGG AGUUAUUAG

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68817
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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