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- EMDB-77176: VIPR Ternary Complex with a pre-unwound dsDNA substrate, 11 subunits -

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Basic information

Entry
Database: EMDB / ID: EMD-77176
TitleVIPR Ternary Complex with a pre-unwound dsDNA substrate, 11 subunits
Map dataSharpened Map
Sample
  • Complex: Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA substrate, showing 11 subunits.
    • Protein or peptide: SUSP1 Vipr Protein
    • DNA: Target DNA strand
    • RNA: RNA (88-MER)
    • DNA: DNA (45-MER)
KeywordsRibonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesSuspvirus SUSP1 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsDocter TA / Yoon PH / Zhang Z / Brohawn SG / Doudna JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF 2334028 United States
CitationJournal: Science / Year: 2026
Title: VIPR RNA-guided DNA recognition by noncontiguous geometric triplex formation
Authors: Yoon PH / Docter TA / Zhang ZT / Loi K / Lopez SC / Valentin-Alvarado LE / Tuck O / Brohawn SG / Doudna JA
History
DepositionMay 15, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77176.png

Downloads & links

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Map

FileDownload / File: emd_77176.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 336 pix.
= 383.04 Å		1.14 Å/pix.
x 336 pix.
= 383.04 Å		1.14 Å/pix.
x 336 pix.
= 383.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0494
Minimum - Maximum-0.47722438 - 0.7328428
Average (Standard dev.)0.00013282672 (±0.013851311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 383.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_77176_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_77176_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_77176_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA...

EntireName: Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA substrate, showing 11 subunits.
Components
  • Complex: Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA substrate, showing 11 subunits.
    • Protein or peptide: SUSP1 Vipr Protein
    • DNA: Target DNA strand
    • RNA: RNA (88-MER)
    • DNA: DNA (45-MER)

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Supramolecule #1: Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA...

SupramoleculeName: Ternary complex of the SUSP1 VIPR system with a pre-unwound dsDNA substrate, showing 11 subunits.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Suspvirus SUSP1

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Macromolecule #1: SUSP1 Vipr Protein

MacromoleculeName: SUSP1 Vipr Protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Suspvirus SUSP1
Molecular weightTheoretical: 22.979531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLLNIKITG TRPFLSHADT LSDPLNPLTK YHKSLSSKRK KTDEDYALLA ESQLVTSCYY DEQLGFVMNG EMIEACIKSG AKLNKLGKV IDRAIMLTDV VFPMTIKNCP ANPQELAKNQ DFIYAKSVKI GTARVMSYRP IFRDWSVEFG LMFDEEQITK E ELLMVLEN ...String:
MKLLNIKITG TRPFLSHADT LSDPLNPLTK YHKSLSSKRK KTDEDYALLA ESQLVTSCYY DEQLGFVMNG EMIEACIKSG AKLNKLGKV IDRAIMLTDV VFPMTIKNCP ANPQELAKNQ DFIYAKSVKI GTARVMSYRP IFRDWSVEFG LMFDEEQITK E ELLMVLEN AGNLCGVGDW RPRFGRFSVE IMSEGNVENL YFQS

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Macromolecule #2: Target DNA strand

MacromoleculeName: Target DNA strand / type: dna / ID: 2 / Details: Resolvable segment of the target DNA strand / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.63159 KDa
SequenceString: (DA)(DT)(DT)(DT)(DA)(DG)(DA)(DC)(DG)(DT) (DT)(DA)(DG)(DC)(DG)(DA)(DC)(DG)(DA)(DG) (DG)(DA)(DA)(DG)(DT)(DA)(DG)(DT)(DT) (DG)(DC)(DC)(DG)(DG)(DC)(DG)(DT)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DG)(DT) ...String:
(DA)(DT)(DT)(DT)(DA)(DG)(DA)(DC)(DG)(DT) (DT)(DA)(DG)(DC)(DG)(DA)(DC)(DG)(DA)(DG) (DG)(DA)(DA)(DG)(DT)(DA)(DG)(DT)(DT) (DG)(DC)(DC)(DG)(DG)(DC)(DG)(DT)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DG)(DT)(DT)(DG) (DA)(DC)(DG)(DT)(DA)(DG)(DC)(DA)(DA)(DT) (DT)(DA) (DA)(DA)(DC)

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Macromolecule #4: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 4
Details: Resolvable segment of the non-target strand from the pre-unwound dsDNA substrate.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.309367 KDa
SequenceString: (DG)(DT)(DT)(DT)(DA)(DA)(DT)(DT)(DG)(DC) (DT)(DA)(DC)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DC)(DC)(DT)(DC)(DA)(DG)(DA)(DC)(DA) (DT)(DG)(DA)(DC)(DT)(DC)(DA)(DT)(DC)(DG) (DC) (DA)(DG)(DG)(DT)(DG)(DG) ...String:
(DG)(DT)(DT)(DT)(DA)(DA)(DT)(DT)(DG)(DC) (DT)(DA)(DC)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DC)(DC)(DT)(DC)(DA)(DG)(DA)(DC)(DA) (DT)(DG)(DA)(DC)(DT)(DC)(DA)(DT)(DC)(DG) (DC) (DA)(DG)(DG)(DT)(DG)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DA)(DA)(DC)(DG)(DT)(DC) (DT)(DA) (DA)(DA)(DT)

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Macromolecule #3: RNA (88-MER)

MacromoleculeName: RNA (88-MER) / type: rna / ID: 3 / Details: Resolvable segment of the SUSP1 Vipr vrRNA. / Number of copies: 1
Source (natural)Organism: Suspvirus SUSP1
Molecular weightTheoretical: 30.630064 KDa
SequenceString:
UAUGGUAAGG UGUGGUUCGG UAAGGUGCGG UGGGGUAAGG CUAGGUUUGG UCUGGUGUGG GUGGAUGGUA GUAGCCACGU UAAAAAUCU ACCAA

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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: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / 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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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