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- EMDB-77733: P. fulva VIPR Ternary Complex with four subunits -

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Basic information

Entry
Database: EMDB / ID: EMD-77733
TitleP. fulva VIPR Ternary Complex with four subunits
Map dataSharpened Map
Sample
  • Complex: Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 4 subunits.
    • RNA: Target Strand
    • RNA: viprRNA
    • Protein or peptide: Vipr protein
  • Ligand: water
KeywordsRibonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA complex
Biological speciesunidentified (others) / Escherichia coli (E. coli) / Pseudomonas fulva (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 24, 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_77733.png

Downloads & links

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Map

FileDownload / File: emd_77733.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: 0.258
Minimum - Maximum-1.9766762 - 3.0579586
Average (Standard dev.)-0.0005877503 (±0.04567953)
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_77733_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_77733_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_77733_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 a P. fulva prophage VIPR system with an unknow...

EntireName: Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 4 subunits.
Components
  • Complex: Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 4 subunits.
    • RNA: Target Strand
    • RNA: viprRNA
    • Protein or peptide: Vipr protein
  • Ligand: water

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

SupramoleculeName: Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 4 subunits.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: unidentified (others) / Strain: Pseudomonas fulva prophage

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Macromolecule #1: Target Strand

MacromoleculeName: Target Strand / type: rna / ID: 1
Details: Unknown host genomic sequence. Modeled to match vrRNA.
Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.66512 KDa
SequenceString:
CUUUUUUUCG CU

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Macromolecule #2: viprRNA

MacromoleculeName: viprRNA / type: rna / ID: 2
Details: Segment of P. fulva prophage viprRNA. Base assignment done by density, no clear sequence was resolvable within the data.
Number of copies: 1
Source (natural)Organism: Pseudomonas fulva (bacteria)
Molecular weightTheoretical: 6.548024 KDa
SequenceString:
CAUGGCAAGG CAAGGCAAGG

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Macromolecule #3: Vipr protein

MacromoleculeName: Vipr protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / 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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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 210297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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