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- EMDB-55046: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-55046
TitleCryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
Map data
Sample
  • Complex: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Dynein axonemal assembly factor 19
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHSP90 Chaperone complex / CHAPERONE
Function / homology
Function and homology information


determination of digestive tract left/right asymmetry / epithelial cilium movement involved in determination of left/right asymmetry / axonemal dynein complex assembly / outer dynein arm assembly / inner dynein arm assembly / epithelial cilium movement involved in extracellular fluid movement / outer dynein arm / cilium movement / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body ...determination of digestive tract left/right asymmetry / epithelial cilium movement involved in determination of left/right asymmetry / axonemal dynein complex assembly / outer dynein arm assembly / inner dynein arm assembly / epithelial cilium movement involved in extracellular fluid movement / outer dynein arm / cilium movement / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / RPAP3/R2TP/prefoldin-like complex / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / R2TP complex / dynein axonemal particle / determination of left/right symmetry / Swr1 complex / establishment of protein localization to chromatin / Ino80 complex / motile cilium / regulation of double-strand break repair / box C/D snoRNP assembly / heart looping / NuA4 histone acetyltransferase complex / regulation of chromosome organization / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / Telomere Extension By Telomerase / protein folding chaperone complex / axoneme / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of double-strand break repair via homologous recombination / regulation of embryonic development / telomere maintenance / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / : / DNA helicase activity / cellular response to estradiol stimulus / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / euchromatin / ADP binding / beta-catenin binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / nuclear matrix / positive regulation of canonical Wnt signaling pathway / cellular response to UV / transcription corepressor activity / nucleosome / UCH proteinases / HATs acetylate histones / ATPase binding / DNA recombination / protein folding / ciliary basal body / spermatogenesis / DNA helicase / regulation of apoptotic process / regulation of cell cycle / transcription coactivator activity / nuclear speck / protein stabilization / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / cadherin binding / ribonucleoprotein complex / DNA repair / centrosome / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / ATP hydrolysis activity / DNA-templated transcription / extracellular exosome / nucleoplasm / extracellular region / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dynein attachment factor, N-terminal / Coiled-coil domain-containing protein 103 / Dynein attachment factor N-terminus / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain ...Dynein attachment factor, N-terminal / Coiled-coil domain-containing protein 103 / Dynein attachment factor N-terminus / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein axonemal assembly factor 19 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMunoz-Hernandez H / Wieczorek M / Pal M
Funding support United Kingdom, Switzerland, 6 items
OrganizationGrant numberCountry
Royal SocietyRG/R2/232314 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X511158/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X502753/1 United Kingdom
Wellcome Trust210719/Z/18/Z/18/Z United Kingdom
Swiss National Science Foundation310030_208120 Switzerland
Swiss National Science FoundationTMSGI3_211309 Switzerland
CitationJournal: To Be Published
Title: CCDC103-mediated assembly of the R2C complex links RUVBL1-RUVBL2 to Primary Ciliary Dyskinesia
Authors: Munoz-Hernandez H / Wieczorek M / Pal M
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55046.png

Downloads & links

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Map

FileDownload / File: emd_55046.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.097475946 - 0.2932735
Average (Standard dev.)0.0018163602 (±0.008778441)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55046_additional_1.map
Projections & Slices
AxesZYX

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Additional map: #2

Fileemd_55046_additional_2.map
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Histogram

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Half map: #2

Fileemd_55046_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55046_half_map_2.map
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Sample components

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Entire : Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex

EntireName: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
Components
  • Complex: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Dynein axonemal assembly factor 19
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex

SupramoleculeName: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.072801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH HHSSGENLYF QGSHMKIEEV KSTTKTQRIA SHSHVKGLGL DESGLAKQAA SGLVGQENAR EACGVIVELI KSKKMAGRA VLLAGPPGTG KTALALAIAQ ELGSKVPFCP MVGSEVYSTE IKKTEVLMEN FRRAIGLRIK ETKEVYEGEV T ELTPCETE ...String:
MGSSHHHHHH HHSSGENLYF QGSHMKIEEV KSTTKTQRIA SHSHVKGLGL DESGLAKQAA SGLVGQENAR EACGVIVELI KSKKMAGRA VLLAGPPGTG KTALALAIAQ ELGSKVPFCP MVGSEVYSTE IKKTEVLMEN FRRAIGLRIK ETKEVYEGEV T ELTPCETE NPMGGYGKTI SHVIIGLKTA KGTKQLKLDP SIFESLQKER VEAGDVIYIE ANSGAVKRQG RCDTYATEFD LE AEEYVPL PKGDVHKKKE IIQDVTLHDL DVANARPQGG QDILSMMGQL MKPKKTEITD KLRGEINKVV NKYIDQGIAE LVP GVLFVD EVHMLDIECF TYLHRALESS IAPIVIFASN RGNCVIRGTE DITSPHGIPL DLLDRVMIIR TMLYTPQEMK QIIK IRAQT EGINISEEAL NHLGEIGTKT TLRYSVQLLT PANLLAKING KDSIEKEHVE EISELFYDAK SSAKILADQQ DKYMK

UniProtKB: RuvB-like 1

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.264609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTSWS HPQFEK

UniProtKB: RuvB-like 2

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Macromolecule #3: Dynein axonemal assembly factor 19

MacromoleculeName: Dynein axonemal assembly factor 19 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.230918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MERNDIINFK ALEKELQAAL TADEKYKREN AAKLRAVEQR VASYEEFRGI VLASHLKPLE RKDKMGGKRT VPWNCHTIQG RTFQDVATE ISPEKAPLQP ETSADFYRDW RRHLPSGPER YQALLQLGGP RLG(CSD)LFQTDV GFGLLGELLV ALADHVG PA DRAAVLGILC ...String:
MERNDIINFK ALEKELQAAL TADEKYKREN AAKLRAVEQR VASYEEFRGI VLASHLKPLE RKDKMGGKRT VPWNCHTIQG RTFQDVATE ISPEKAPLQP ETSADFYRDW RRHLPSGPER YQALLQLGGP RLG(CSD)LFQTDV GFGLLGELLV ALADHVG PA DRAAVLGILC SLASTGRFTL NLSLLSRAER ESCKGLFQKL QAMGNPRSVK EGLSWEEQGL EEQSGGLQEE ERLLQELL E LYQVD

UniProtKB: Dynein axonemal assembly factor 19

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 417820
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9sn2:
Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex

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