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- EMDB-63121: CryoEM Structures Uncover the Unexpected Hinges of IscB for Enhan... -

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Basic information

Entry
Database: EMDB / ID: EMD-63121
TitleCryoEM Structures Uncover the Unexpected Hinges of IscB for Enhanced Gene Editing
Map data
Sample
  • Complex: The ternary complex formed by IscB, wRNA, and Target DNA
    • RNA: RNA (194-MER)
    • DNA: DNA (27-MER)
    • DNA: DNA (26-MER)
    • Protein or peptide: Iscb+Twin-Strep-tag
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsIscB / Target DNA / HNH / DNA BINDING PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHu CY / Wang FZ / Ma SS / Zhang SF
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: CryoEM Structures Uncover the Unexpected Hinges of IscB for Enhanced Gene Editing
Authors: Hu CY / Wang FZ / Ma SS / Zhang SF
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63121.png

Downloads & links

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Map

FileDownload / File: emd_63121.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.)
0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 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: 0.08
Minimum - Maximum-0.18105482 - 0.45904636
Average (Standard dev.)0.00070430257 (±0.018735655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63121_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63121_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63121_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The ternary complex formed by IscB, wRNA, and Target DNA

EntireName: The ternary complex formed by IscB, wRNA, and Target DNA
Components
  • Complex: The ternary complex formed by IscB, wRNA, and Target DNA
    • RNA: RNA (194-MER)
    • DNA: DNA (27-MER)
    • DNA: DNA (26-MER)
    • Protein or peptide: Iscb+Twin-Strep-tag
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: The ternary complex formed by IscB, wRNA, and Target DNA

SupramoleculeName: The ternary complex formed by IscB, wRNA, and Target DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: RNA (194-MER)

MacromoleculeName: RNA (194-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 62.54618 KDa
SequenceString: UCUAUAUCAU GGCCGAGGCU CUUCCAACUG CGGGUUGAAA GAGCACAGGC UGAGACAUUC GUAAGGCCGA AAGGCCGGAC GCACCCUGG GAUUUCCCCA GUCCCCGGAA CUGCAUAGCG GAUGCCAGUU GAUGGAGCAA UCUAUCAGAU AAGCCAGGGG G AACAAUCA ...String:
UCUAUAUCAU GGCCGAGGCU CUUCCAACUG CGGGUUGAAA GAGCACAGGC UGAGACAUUC GUAAGGCCGA AAGGCCGGAC GCACCCUGG GAUUUCCCCA GUCCCCGGAA CUGCAUAGCG GAUGCCAGUU GAUGGAGCAA UCUAUCAGAU AAGCCAGGGG G AACAAUCA CCUCUCUGUA UCAGAGAGAG UUUUAC

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Macromolecule #2: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.387404 KDa
SequenceString:
(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DT)(DT) (DG)(DT)(DC)(DG)(DG)(DC)(DC)(DA)(DT)(DG) (DA)(DT)(DA)(DT)(DA)(DG)(DA)

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Macromolecule #3: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.90112 KDa
SequenceString:
(DG)(DA)(DT)(DA)(DT)(DA)(DG)(DT)(DA)(DC) (DC)(DG)(DG)(DC)(DT)(DC)(DA)(DA)(DC)(DC) (DA)(DC)(DC)(DT)(DA)(DC)

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Macromolecule #4: Iscb+Twin-Strep-tag

MacromoleculeName: Iscb+Twin-Strep-tag / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: MAGNESIUM ION

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

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36751
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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