[English] 日本語
Yorodumi
- PDB-29jr: Cryo-EM structure of human CCDC103/DNAAF19 in complex with RUVBL1/2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29jr
TitleCryo-EM structure of human CCDC103/DNAAF19 in complex with RUVBL1/2
Components
  • Dynein axonemal assembly factor 19
  • RuvB-like 1
  • RuvB-like 2
KeywordsCHAPERONE / Motile cilia / Axonemal dynein assembly factors / AAA-ATPases
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: 3.47 Å
AuthorsWood, E. / Ochi, T.
Funding support United Kingdom, 1items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)336,37313
Polymers333,8097
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

-
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: 50296.914 Da / Num. of mol.: 1
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: 51222.465 Da / Num. of mol.: 5
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: 27400.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAAF19, CCDC103 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IW40
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: CCDC103-RUVBL1/2 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
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.21.1_5286model refinement
5CTFFINDCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 817388
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100791 / Symmetry type: POINT
Atomic model buildingB value: 105.2 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more