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- EMDB-77745: P. fulva VIPR Ternary Complex Consensus Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-77745
TitleP. fulva VIPR Ternary Complex Consensus Conformation
Map dataSharpened Map
Sample
  • Complex: Consensus Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 10 subunits.
    • RNA: viprRNA
    • DNA: Target DNA
    • DNA: Non-target DNA
    • Protein or peptide: P. fulva prophage protein
KeywordsRibonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesPseudomonas fulva (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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
DepositionJun 25, 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_77745.png

Downloads & links

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Map

FileDownload / File: emd_77745.map.gz / Format: CCP4 / Size: 125 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.)
0.94 Å/pix.
x 320 pix.
= 301.824 Å		0.94 Å/pix.
x 320 pix.
= 301.824 Å		0.94 Å/pix.
x 320 pix.
= 301.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9432 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.686275 - 1.1348419
Average (Standard dev.)-0.00018079593 (±0.024262533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 301.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_77745_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_77745_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_77745_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 : Consensus Ternary complex of a P. fulva prophage VIPR system with...

EntireName: Consensus Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 10 subunits.
Components
  • Complex: Consensus Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 10 subunits.
    • RNA: viprRNA
    • DNA: Target DNA
    • DNA: Non-target DNA
    • Protein or peptide: P. fulva prophage protein

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Supramolecule #1: Consensus Ternary complex of a P. fulva prophage VIPR system with...

SupramoleculeName: Consensus Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 10 subunits.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas fulva (bacteria)

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Macromolecule #1: viprRNA

MacromoleculeName: viprRNA / type: rna / ID: 1 / Details: Resolvable segment of P. fulva prophage viprRNA. / Number of copies: 1
Source (natural)Organism: Pseudomonas fulva (bacteria)
Molecular weightTheoretical: 17.098258 KDa
SequenceString:
GGUAAGGUCC GGUCCGGUAA GGUAAGGUAA GGCAAGGUAA GGUAAGGUAA GG

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Macromolecule #2: Target DNA

MacromoleculeName: Target DNA / type: dna / ID: 2
Details: Segment of an unknown target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as ...Details: Segment of an unknown target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as complementary to the vrRNA with x3 bases being treated as cytosines or guanines as density permitted. The non-target strand was modeled largely as thymines, with intermittent guanines and cytosines as density permitted.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.280916 KDa
SequenceString:
(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DC)(DT) (DT)(DC)(DT)(DT)(DG)(DT)(DT)(DG)(DG)(DG) (DC)(DG)(DG)(DG)(DT)(DT)(DC)(DG)(DG) (DC)

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Macromolecule #3: Non-target DNA

MacromoleculeName: Non-target DNA / type: dna / ID: 3
Details: Segment of an unknown non-target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as ...Details: Segment of an unknown non-target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as complementary to the vrRNA with x3 bases being treated as cytosines or guanines as density permitted. The non-target strand was modeled largely as thymines, with intermittent guanines and cytosines as density permitted.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.196351 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DC) (DT)(DT)(DC)(DT)(DT)(DG)(DT)

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Macromolecule #4: P. fulva prophage protein

MacromoleculeName: P. fulva prophage protein / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas fulva (bacteria)
Molecular weightTheoretical: 24.085209 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQTLKVKIVG TRPLLVHADV FADPLNKLTK SHKQLTSKRK KSDEDHELIA RSEWRGGLYF SEDVGPYLPG INIESALVAG GKLSKMGTQ LKRSVEIMDT RCPIIYEGPR SVEGLWDEQF YDARSVKVGT ARITRYRPLF RSWAVVCEIA YDQESIDRDQ V LKCLEDAG ...String:
MQTLKVKIVG TRPLLVHADV FADPLNKLTK SHKQLTSKRK KSDEDHELIA RSEWRGGLYF SEDVGPYLPG INIESALVAG GKLSKMGTQ LKRSVEIMDT RCPIIYEGPR SVEGLWDEQF YDARSVKVGT ARITRYRPLF RSWAVVCEIA YDQESIDRDQ V LKCLEDAG QYCGVGDYRP KFGRFAVEVL NSSSNNNNNN NNNNLGIEEN LYFQ

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.6 µm / Nominal defocus min: 0.6 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95999
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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