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- EMDB-57241: Composite cryo-EM map of the human DNAAF19-RUVBL1/2-DPCD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-57241
TitleComposite cryo-EM map of the human DNAAF19-RUVBL1/2-DPCD complex
Map dataComposite map of human DNAAF19-RUVBL1/2-DPCD
Sample
  • Complex: Ternary complex comprised of RUVBL1, RUVBL2, DNAAF19, DPCD
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Dynein axonemal assembly factor 19
    • Protein or peptide: Protein DPCD
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMotile cilia / protein complex assembly / Dynein axonemal assembly factor / 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
Protein DPCD / DPCD protein family / 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 ...Protein DPCD / DPCD protein family / 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 / Protein DPCD / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWood E / Ochi T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: DNAAF19-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 / Beyer T / Khan GN / Mitchison H / Ochi T
History
DepositionMar 18, 2026-
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_57241.png

Downloads & links

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Map

FileDownload / File: emd_57241.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of human DNAAF19-RUVBL1/2-DPCD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 5.0
Minimum - Maximum-9.931487000000001 - 29.020092000000002
Average (Standard dev.)0.0036430215 (±1.0554532)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Dynein axonemal assembly factor 19
    • Protein or peptide: Protein DPCD
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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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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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

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: 5 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 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 KGETMDTS

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
Details: Three residual residues (GGS) after removing a N-terminal lipoyl tag.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.400104 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGSMERNDII NFKALEKELQ AALTADEKYK RENAAKLRAV EQRVASYEEF RGIVLASHLK PLERKDKMGG KRTVPWNCHT IQGRTFQDV ATEISPEKAP LQPETSADFY RDWRRHLPSG PERYQALLQL GGPRLGCLFQ TDVGFGLLGE LLVALADHVG P ADRAAVLG ...String:
GGSMERNDII NFKALEKELQ AALTADEKYK RENAAKLRAV EQRVASYEEF RGIVLASHLK PLERKDKMGG KRTVPWNCHT IQGRTFQDV ATEISPEKAP LQPETSADFY RDWRRHLPSG PERYQALLQL GGPRLGCLFQ TDVGFGLLGE LLVALADHVG P ADRAAVLG ILCSLASTGR FTLNLSLLSR AERESCKGLF QKLQAMGNPR SVKEGLSWEE QGLEEQSGGL QEEERLLQEL LE LYQVD

UniProtKB: Dynein axonemal assembly factor 19

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Macromolecule #4: Protein DPCD

MacromoleculeName: Protein DPCD / type: protein_or_peptide / ID: 4
Details: Two residual residues (GS) after removing a N-terminal GST tag.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.420926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMAVTGWLE SLRTAQKTAL LQDGRRKVHY LFPDGKEMAE EYDEKTSELL VRKWRVKSAL GAMGQWQLEV GDPAPLGAGN LGPELIKES NANPIFMRKD TKMSFQWRIR NLPYPKDVYS VSVDQKERCI IVRTTNKKYY KKFSIPDLDR HQLPLDDALL S FAHANCTL ...String:
GSMAVTGWLE SLRTAQKTAL LQDGRRKVHY LFPDGKEMAE EYDEKTSELL VRKWRVKSAL GAMGQWQLEV GDPAPLGAGN LGPELIKES NANPIFMRKD TKMSFQWRIR NLPYPKDVYS VSVDQKERCI IVRTTNKKYY KKFSIPDLDR HQLPLDDALL S FAHANCTL IISYQKPKEV VVAESELQKE LKKVKTAHSN DGDCKTQ

UniProtKB: Protein DPCD

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / 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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
250.0 mMNaClSodium chloride
2.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec. / Pretreatment - Atmosphere: AIR
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.21.1) / Number images used: 363543
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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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
Output model

PDB-29kn:
Composite cryo-EM map of the human DNAAF19-RUVBL1/2-DPCD complex

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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
Output model

PDB-29kn:
Composite cryo-EM map of the human DNAAF19-RUVBL1/2-DPCD complex

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