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- EMDB-57221: Focused map of the external DII domain of RUVBL2 in complex with DPCD -

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Basic information

Entry
Database: EMDB / ID: EMD-57221
TitleFocused map of the external DII domain of RUVBL2 in complex with DPCD
Map dataFocused map of the external DII domain of RUVBL2 in complex with DPCD
Sample
  • Complex: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD
KeywordsMotile cilia / protein complex assembly / Dynein axonemal assembly factor / CHAPERONE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsWood E / Ochi T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published / Year: 2026
Title: CCDC103-RUVBL1/2 complex recruits multiple adaptors to promote dynein arm assembly
Authors: de Almeida Gomes M / Wood E / Burgoyne T / Batrinu D / Klose F / Boldt K / Khan G / Mitchison H / Ochi T
History
DepositionMar 17, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57221.png

Downloads & links

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Map

FileDownload / File: emd_57221.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the external DII domain of RUVBL2 in complex with DPCD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 230 pix.
= 340.4 Å		1.48 Å/pix.
x 230 pix.
= 340.4 Å		1.48 Å/pix.
x 230 pix.
= 340.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2003956 - 2.8977141
Average (Standard dev.)-0.00065960415 (±0.061332345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 340.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_57221_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_57221_half_map_2.map
AnnotationHalf map B
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 comprised of RUVBL1, RUVBL2, DNAAF19, DPCD

EntireName: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD
Components
  • Complex: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD

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Supramolecule #1: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD

SupramoleculeName: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
250.0 mMNaClSodium chloride
2.0 mMC4H10O2S2DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 239741
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 6 / Avg.num./class: 60590 / Software - Name: RELION (ver. 5)
Details: Focused 3D classification around the DPCD and the external DII domain of hRUVBL2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

29jr


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsDNAAF19-RUVBL1/2 without their external DII domains
RefinementProtocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsThe external DII domains of RUVBL2 in complex with DPCD
RefinementProtocol: AB INITIO MODEL

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