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

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Basic information

Entry
Database: PDB / ID: 9sn2
TitleCryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
Components
  • Dynein axonemal assembly factor 19
  • RuvB-like 1
  • RuvB-like 2
KeywordsCHAPERONE / HSP90 Chaperone complex
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
ADENOSINE-5'-DIPHOSPHATE / Dynein axonemal assembly factor 19 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMunoz-Hernandez, H. / Wieczorek, M. / Pal, M.
Funding support United Kingdom, Switzerland, 6items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RuvB-like 1
D: RuvB-like 2
G: Dynein axonemal assembly factor 19
B: RuvB-like 1
C: RuvB-like 1
E: RuvB-like 2
F: RuvB-like 2
H: Dynein axonemal assembly factor 19
I: Dynein axonemal assembly factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,26815
Polymers397,7059
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein RuvB-like 1 / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 53072.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y265, DNA helicase
#2: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 52264.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y230, DNA helicase
#3: Protein Dynein axonemal assembly factor 19 / Coiled-coil domain-containing protein 103


Mass: 27230.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAAF19, CCDC103 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IW40
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12cryoSPARC43D reconstruction
13PHENIX2.0_5750model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 417820 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 94.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003720379
ELECTRON MICROSCOPYf_angle_d0.846827501
ELECTRON MICROSCOPYf_chiral_restr0.05013210
ELECTRON MICROSCOPYf_plane_restr0.00623522
ELECTRON MICROSCOPYf_dihedral_angle_d11.91362876

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