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- EMDB-63122: CryoEM Structures Uncover the Unexpected Hinges of IscB for Enhan... -

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Basic information

Entry
Database: EMDB / ID: EMD-63122
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*CP*TP*CP*AP*AP*CP*CP*AP*CP*CP*TP*AP*C)-3')
    • DNA: DNA (5'-D(P*CP*TP*AP*GP*GP*TP*GP*GP*TP*TP*GP*TP*CP*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: 3.39 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_63122.png

Downloads & links

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Map

FileDownload / File: emd_63122.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: 0.061
Minimum - Maximum-0.1921407 - 0.45455813
Average (Standard dev.)0.00075246673 (±0.014613703)
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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Half map: #2

Fileemd_63122_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_63122_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 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*CP*TP*CP*AP*AP*CP*CP*AP*CP*CP*TP*AP*C)-3')
    • DNA: DNA (5'-D(P*CP*TP*AP*GP*GP*TP*GP*GP*TP*TP*GP*TP*CP*GP*GP*CP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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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-#4
Source (natural)Organism: synthetic construct (others)

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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: 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 #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

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

MacromoleculeName: DNA (5'-D(P*CP*TP*CP*AP*AP*CP*CP*AP*CP*CP*TP*AP*C)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.840528 KDa
SequenceString:
(DC)(DT)(DC)(DA)(DA)(DC)(DC)(DA)(DC)(DC) (DT)(DA)(DC)

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Macromolecule #4: DNA (5'-D(P*CP*TP*AP*GP*GP*TP*GP*GP*TP*TP*GP*TP*CP*GP*GP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*CP*TP*AP*GP*GP*TP*GP*GP*TP*TP*GP*TP*CP*GP*GP*CP*C)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.250381 KDa
SequenceString:
(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DT)(DT) (DG)(DT)(DC)(DG)(DG)(DC)(DC)

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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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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 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 / Chamber humidity: 100 %

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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

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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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 318267
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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