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- EMDB-57214: Cryo-EM structure of human CCDC103/DNAAF19 in complex with RUVBL1/2 -

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Basic information

Entry
Database: EMDB / ID: EMD-57214
TitleCryo-EM structure of human CCDC103/DNAAF19 in complex with RUVBL1/2
Map data
Sample
  • Complex: CCDC103-RUVBL1/2 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
KeywordsMotile cilia / Axonemal dynein assembly factors / AAA-ATPases / 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: 3.47 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_57214.png

Downloads & links

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Map

FileDownload / File: emd_57214.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.8958416 - 1.4831389
Average (Standard dev.)0.0060091177 (±0.055356793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57214_msk_1.map
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Additional map: #1

Fileemd_57214_additional_1.map
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Half map: #2

Fileemd_57214_half_map_1.map
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Half map: #1

Fileemd_57214_half_map_2.map
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Sample components

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Entire : CCDC103-RUVBL1/2 complex

EntireName: CCDC103-RUVBL1/2 complex
Components
  • Complex: CCDC103-RUVBL1/2 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: CCDC103-RUVBL1/2 complex

SupramoleculeName: CCDC103-RUVBL1/2 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: 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 / 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: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 817388
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Four ab-initio models were generated using cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100791
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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 / Overall B value: 105.2 / Target criteria: Cross-correlation coefficient
Output model

PDB-29jr:
Cryo-EM structure of human CCDC103/DNAAF19 in complex with RUVBL1/2

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