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- EMDB-75700: Engineered IscB and wRNA bound to Target ssDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-75700
TitleEngineered IscB and wRNA bound to Target ssDNA
Map data
Sample
  • Complex: Engineered IscB and wRNA bound to Target ssDNA
    • Protein or peptide: IscB
    • RNA: RNA (233-MER)
    • DNA: Target ssDNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsIscB / Cas9 / HNH / CRISPR-Cas / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXu C / Yang Q / Niu X / Ke A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35118174 United States
CitationJournal: To Be Published
Title: engineered IscB-OMEGA RNA-ssDNA complex
Authors: Xu C / Yang Q / Niu X / Ke A
History
DepositionFeb 25, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75700.png

Downloads & links

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Map

FileDownload / File: emd_75700.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 231. Å		0.83 Å/pix.
x 280 pix.
= 231. Å		0.83 Å/pix.
x 280 pix.
= 231. 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: 0.03
Minimum - Maximum-0.2208232 - 0.57246965
Average (Standard dev.)-0.00023889495 (±0.013632055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75700_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75700_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 : Engineered IscB and wRNA bound to Target ssDNA

EntireName: Engineered IscB and wRNA bound to Target ssDNA
Components
  • Complex: Engineered IscB and wRNA bound to Target ssDNA
    • Protein or peptide: IscB
    • RNA: RNA (233-MER)
    • DNA: Target ssDNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Engineered IscB and wRNA bound to Target ssDNA

SupramoleculeName: Engineered IscB and wRNA bound to Target ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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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: 56.779602 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAVVYVISKS GKPLMPTTRC GHVRILLKEG KARVVERKPF TIQLTYESAE ETQPLVLGID PGRTNIGMSV VTESGESVFN AQLETRNKD VPKLMKDRKQ YRRAHRRLKR RSKRRRRAKA AGTAFEEGEK QRLLPGCKKP ITCKSIRNKE ARFNNRKRPK G WLTPTANH ...String:
MAVVYVISKS GKPLMPTTRC GHVRILLKEG KARVVERKPF TIQLTYESAE ETQPLVLGID PGRTNIGMSV VTESGESVFN AQLETRNKD VPKLMKDRKQ YRRAHRRLKR RSKRRRRAKA AGTAFEEGEK QRLLPGCKKP ITCKSIRNKE ARFNNRKRPK G WLTPTANH LLVTHLNVVK KVQKILPVAK VVLELNRFSF MAMNNPKVQR WQYQRGPLYG KGSVEEAVSM QQDGHCLFCK HG IDHYHHV VPRRKNGSET LENRVGLCEE HHRLVHTDKE WEARLASKKS GMNKKYHALS VLNQIIPYLA DQLADMFPGN FSV TSGRDT RLFREEHGIP KDHYLDAYCI ACSALTDAKK VSSPKGRPYM VRQFRRHDRQ ASHKANLNRS YYMGGKKVAT NRHK AMDQK TDSLEEYRAA HSAADVSKLT VKHPSAQYKD MSRIMPGSIL VSGEGKLFTL SRSEGRNKGQ VNYFVSTEGI KYWAR KCQY LRNNGGLQIY V

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Macromolecule #2: RNA (233-MER)

MacromoleculeName: RNA (233-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 75.414812 KDa
SequenceString: AAAAGAGUGA ACGAGAGGCU CUUUCAACUU GAAAAGGUUG AAAGAGCACA GGCUGAGACA UUCGUAAGGC CGAAAGGCCG GACGCACCC UGGGAUUUCC CCAGUCCCCG GAACUGCAUA GCGGAUGUCA GUUGAUCGGC CGAGUAAUUU ACGUCGACGU U GACGUCGA ...String:
AAAAGAGUGA ACGAGAGGCU CUUUCAACUU GAAAAGGUUG AAAGAGCACA GGCUGAGACA UUCGUAAGGC CGAAAGGCCG GACGCACCC UGGGAUUUCC CCAGUCCCCG GAACUGCAUA GCGGAUGUCA GUUGAUCGGC CGAGUAAUUU ACGUCGACGU U GACGUCGA UGGUUGCGGC CGAUCAGAUA AGCCAGGGGG AACAAUCACC UCUCUGGAAA CAGAGAGAGU UUUAC

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Macromolecule #3: Target ssDNA

MacromoleculeName: Target ssDNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.405396 KDa
SequenceString:
(DT)(DC)(DT)(DT)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DG)(DT)(DT)(DC)(DA)(DC)(DT)(DC) (DT)(DT)(DT)(DT)(DC)(DT)(DC)(DT)

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

Particle selectionNumber selected: 6173103
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 293636
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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