[English] 日本語
Yorodumi
- EMDB-63120: CryoEM Structures Uncover the Unexpected Hinges of IscB for Enhan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63120
TitleCryoEM Structures Uncover the Unexpected Hinges of IscB for Enhanced Gene Editing
Map data
Sample
  • Complex: The binary complex of ISCB and wRNA
    • Protein or peptide: Iscb
    • RNA: RNA (190-MER)
    • DNA: DNA (5'-D(P*GP*GP*CP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsIscb / HNH / RNA BINDING PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHu CY / Wang FZ / Ma SS / Zhang SF
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structural insight into IscB's RNA-lid-based inactivation mechanism.
Authors: Feizuo Wang / Ruochen Guo / Senfeng Zhang / Yinuo Cui / Junlan Wang / Tao Hu / Kunming Liu / Qi Wang / Yao Liu / Ki Hyun Nam / Ziqing Winston Zhao / Quanquan Ji / Xin Xu / Ercheng Wang / ...Authors: Feizuo Wang / Ruochen Guo / Senfeng Zhang / Yinuo Cui / Junlan Wang / Tao Hu / Kunming Liu / Qi Wang / Yao Liu / Ki Hyun Nam / Ziqing Winston Zhao / Quanquan Ji / Xin Xu / Ercheng Wang / Youyuan Zhu / Yao Yang / Min Luo / Peixiang Ma / Shengsheng Ma / Chunlong Xu / Chunyi Hu /
Abstract: IscB, a compact Cas9 ancestor from the obligate mobile element guided activity system, has attracted growing interest as a programmable genome editor because of its small size and therapeutic ...IscB, a compact Cas9 ancestor from the obligate mobile element guided activity system, has attracted growing interest as a programmable genome editor because of its small size and therapeutic delivery potential. Despite its promise, structural insights into IscB's regulation remain limited, with only a target-bound R-loop structure previously reported. Here, we present the structural trajectory of an engineered IscB, capturing its transition from a resting state to activation. Using cryo-electron microscopy, we resolve four high-resolution structures: the apo resting state, two intermediate complexes with 6-nt and 10-nt guide-target pairing and a fully paired 16-nt primed cleavage state. These structures uncover a dual inactivation mechanism mediated by RNA lids; the ωRNA lid blocks HNH domain access, while the guide RNA lid occludes the RuvC active site. As guide-target pairing progresses, the guide RNA undergoes a stepwise displacement, mimicking a 'car pedal' motion that triggers activation at 11-nt pairing. The HNH domain also contributes to R-loop stabilization through a positively charged R-wedge motif and undergoes a ~90° activation-driven rotation mediated by two hinge regions. In variants IscBHig1 and IscBHig2, engineering these hinge motifs to enhance conformational flexibility notably improved genome-editing efficiency in cells. In summary, our study reveals the molecular basis underlying IscB autoinhibition and activation, identifies previously uncharacterized regulatory features and establishes hinge elements as a target region for engineering compact, efficient genome editors.
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63120.png

Downloads & links

-
Map

FileDownload / File: emd_63120.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 320.256 Å		0.83 Å/pix.
x 384 pix.
= 320.256 Å		0.83 Å/pix.
x 384 pix.
= 320.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.95440745 - 1.8730197
Average (Standard dev.)0.00012337028 (±0.024764508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 320.25598 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_63120_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63120_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The binary complex of ISCB and wRNA

EntireName: The binary complex of ISCB and wRNA
Components
  • Complex: The binary complex of ISCB and wRNA
    • Protein or peptide: Iscb
    • RNA: RNA (190-MER)
    • DNA: DNA (5'-D(P*GP*GP*CP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: The binary complex of ISCB and wRNA

SupramoleculeName: The binary complex of ISCB and wRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Iscb

MacromoleculeName: Iscb / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 62.165832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVVYVISKS GKPLMPTTRC GHVRILLKEG KARVVERKPF TIQLTYESAE ETQPLVLGID PGRTNIGMSV VTESGESVFN AQIRTRNKD VPKLMKDRKQ YRMAHRRLKR RCKRRRRAKA AGTAFEEGEK QRLLPGCFKP ITCKSIRNKE ARFNNRKRPV G WLTPTANH ...String:
MAVVYVISKS GKPLMPTTRC GHVRILLKEG KARVVERKPF TIQLTYESAE ETQPLVLGID PGRTNIGMSV VTESGESVFN AQIRTRNKD VPKLMKDRKQ YRMAHRRLKR RCKRRRRAKA AGTAFEEGEK QRLLPGCFKP ITCKSIRNKE ARFNNRKRPV G WLTPTANH LLVTHLNVVK KVQKILPVAK VVLELNRFSF MAMNNPKVQR WQYQRGPLYG KGSVEEAVSM QQDGHCLFCK HG IDHYHHV VPRRKNGSET LENRVGLCEE HHRLVHTDKE WEANLASKKS GMNKKYHALS VLNQIIPYLA DQLADMFPGN FCV TSGQDT YLFREEHGIP KDHYLDAYCI ACSALTDAKK VSSPKGRPYM VRQFRRHDRQ ACHKANLNRR YYMGGKLVAT NRHK AMDQK TDSLEEYRAA HSAADVSKLT VKHPSAQYKD MSRIMPGSIL VSGEGKLFTL RRSEGRNKGQ VNYFVSTEGI KYWAR KCQY LRNNGGLQIY VKNKGGSGKR PAATKKAGQA KKKKGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

-
Macromolecule #2: RNA (190-MER)

MacromoleculeName: RNA (190-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 61.323492 KDa
SequenceString:
UAUCAUGGCC GAGGCUCUUC CAACUGAGGG UUGAAAGAGC ACAGGCUGAG ACAUUCGUAA GGCCGAAAGG CCGGACGCAC CCUGGGAUU UCCCCAGUCC CCGGAACUGC AUAGCGGAUG CCAGUUGAUG GAGCAAUCUA UCAGAUAAGC CAGGGGGAAC A AUCACCUC UCUGUAUCAG AGAGAGUUUU AC

-
Macromolecule #3: DNA (5'-D(P*GP*GP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*GP*GP*CP*C)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.191818 KDa
SequenceString:
(DG)(DG)(DC)(DC)

-
Macromolecule #4: ZINC ION

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

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100520
Initial angle assignmentType: ANGULAR RECONSTITUTION
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