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- EMDB-48315: Dodecameric complex of Aedes aegypti RuvBLs1/2 - C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-48315
TitleDodecameric complex of Aedes aegypti RuvBLs1/2 - C1 symmetry
Map data
Sample
  • Complex: Dodecameric complex of Aedes aegypti RuvBLs1/2
    • Protein or peptide: AaRuvBL1
    • Protein or peptide: AaRuvBL2
KeywordsComplex / ATPase / CHAPERONE
Biological speciesAedes aegypti (yellow fever mosquito)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsQuel NG / Antonio LM / Ramos CHI / Rosa LT
Funding support Brazil, 2 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/08855-4 Brazil
Sao Paulo Research Foundation (FAPESP)2017/26131-5 Brazil
CitationJournal: Int J Biol Macromol / Year: 2025
Title: Aedes aegypti encodes an ATPase-active RUVBL1/2 complex.
Authors: Natália G Quel / Leonardo T Rosa / Larissa M Antonio / Glaucia M S Pinheiro / Leandro R S Barbosa / Walid A Houry / Carlos H I Ramos /
Abstract: RUVBL1 and RUVBL2 proteins assemble into a heterohexameric ring and are essential for DNA repair in prokaryotes and chromatin homeostasis in eukaryotes. These proteins function as potential ...RUVBL1 and RUVBL2 proteins assemble into a heterohexameric ring and are essential for DNA repair in prokaryotes and chromatin homeostasis in eukaryotes. These proteins function as potential chaperones and ATPases. While most studies on eukaryotic RUVBL1/2 proteins have focused on human and yeast orthologs, they have revealed notable differences in conformational dynamics, protein interactions, and ATPase activity between these species. By investigating orthologs in other eukaryotic organisms, conserved features of RUVBL1/2 structure and function can be determined. In this study, we analyzed the genome of Aedes aegypti, a dipteran insect and a vector of Dengue, Zika, and Chikungunya viruses, to identify putative RUVBL1/2 family members. We identified protein sequences corresponding to RUVBL1 and RUVBL2, here named as AaRUVBL1 and AaRUVBL2. Purified recombinant AaRUVBL1/2 was properly folded and formed a hetero-dodecamer in solution. The complex exhibited enzymatic ATPase activity, confirming that these proteins are bona fide AAA+ ATPases. However, mutational analysis revealed that ATPase activity requires both AaRUVBL1 and AaRUVBL2, in contrast to the human ortholog, where RUVBL1 and RUVBL2 alone are active ATPases. To characterize the structure of the AaRUVBL1/2 complex, we combined SAXS and Cryo-EM techniques. Our findings indicate that the complex adopts a dodecameric barrel-shaped complex with a maximum dimension of ∼16 nm. Single particle CryoEM analysis revealed a high degree of conformational heterogeneity, both between hexamer rings linked via the DII domains and among each hexameric ring. Overall, these findings contribute to a broader understanding of RUVBL1/2 proteins, particularly as this represents only the second structurally and functionally characterized RUVBL complex within the Animalia filum.
History
DepositionDec 15, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48315.png

Downloads & links

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Map

FileDownload / File: emd_48315.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.017160267 - 0.11133877
Average (Standard dev.)0.0011347838 (±0.008662238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48315_msk_1.map
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Half map: #1

Fileemd_48315_half_map_1.map
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Half map: #2

Fileemd_48315_half_map_2.map
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Sample components

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Entire : Dodecameric complex of Aedes aegypti RuvBLs1/2

EntireName: Dodecameric complex of Aedes aegypti RuvBLs1/2
Components
  • Complex: Dodecameric complex of Aedes aegypti RuvBLs1/2
    • Protein or peptide: AaRuvBL1
    • Protein or peptide: AaRuvBL2

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Supramolecule #1: Dodecameric complex of Aedes aegypti RuvBLs1/2

SupramoleculeName: Dodecameric complex of Aedes aegypti RuvBLs1/2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Double hexameric ring of alternated RuvBL1 and RuvBL2
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Molecular weightTheoretical: 580 KDa

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Macromolecule #1: AaRuvBL1

MacromoleculeName: AaRuvBL1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPDYDIPT TENLYFQGMK IEEVKSTVKT QRIAAHSHVK GLGLDENGVP LQMAAGLVG QKDAREAAGI VVDLIKSKKM SGRALLLAGP PGTGKTAIAL AIAQELGNKV P FCPMVGSE VFSSEIKKTE VLMENFRRSI GLRIRETKEV YEGEVTELTP ...String:
MGSSHHHHHH SQDPDYDIPT TENLYFQGMK IEEVKSTVKT QRIAAHSHVK GLGLDENGVP LQMAAGLVG QKDAREAAGI VVDLIKSKKM SGRALLLAGP PGTGKTAIAL AIAQELGNKV P FCPMVGSE VFSSEIKKTE VLMENFRRSI GLRIRETKEV YEGEVTELTP VETENPMGGY GK TISNVVI GLKTAKGTKQ LKLDPSIYES LQKEKVEVGD VIYIEANSGA VKRQGRSDTF ATE FDLETE EYVPLPKGDV HKKKEVVQDV TLHDLDVANA RPQGGQDVLS MVGQIMKPKK TEIT DKLRM EINKVVNKYI DQGIAELVPG VLFIDEVHML DLECFTYLHK SLESAIAPIV IFATN RGRC VIRGTDDIIS PHGIPLDLLD RLLIVRTAPY NLSEIEQIIK LRAQTEGLSV EDSAIQ ALS EIGDNTTLRY AVQLLTPAHQ NCKVNGRTQI TKDDIVEVNG LFLDAKRSAK FLQEENT KY MM

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Macromolecule #2: AaRuvBL2

MacromoleculeName: AaRuvBL2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAELDKIEVR DITRIERIGA HSHIRGLGLD DVLEARAVSQ GMVGQKDARR AAGLVVQIVR EGKIAGRCIL LAGEPSTGK TAIAVGMAQA LGNETPFTSM SGSEIYSLEM NKTEALSQAL RKSIGVRIKE ETEIIEGEVV E IQIDRPAS GTGQKVGKVT IKTTDMETNY ...String:
MAELDKIEVR DITRIERIGA HSHIRGLGLD DVLEARAVSQ GMVGQKDARR AAGLVVQIVR EGKIAGRCIL LAGEPSTGK TAIAVGMAQA LGNETPFTSM SGSEIYSLEM NKTEALSQAL RKSIGVRIKE ETEIIEGEVV E IQIDRPAS GTGQKVGKVT IKTTDMETNY DLGNKIIECF MKEKIQAGDV ITIDKASGKV SKLGRSFTRA RD YDATGAQ TRFVQCPEGE LQKRKEVVHT VTLHEIDVIN SRTHGFLALF AGDTGEIKQE VRDQINSKVM EWR EEGKAE INPGVLFIDE AHMLDIECFS FLNRALESDM APVVIMATNR GITKIRGTNY RSPHGIPIDL LDRM IIIRT VPYSAKEIKE ILKIRCEEED CQINNEALMV LGRIATETSL RYAIQSITTA SLVSKRRKAA EITVE DIRK VYSLFLDEKR SSKIMKEYQD EYLFYDDSLS QAEQAMEVET N

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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

Concentration0.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTris-HClTris-HCl
200.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsDouble hexameric ring of alternated RuvBL1 and RuvBL2

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Spherical Aberration Constant (Cs) = 0.0001
Image recordingFilm or detector model: GATAN K3 (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: 2.8000000000000003 µm / Nominal defocus min: 1.3 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: NONE
Final reconstructionNumber classes used: 4 / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66892
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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