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- EMDB-52013: Hexameric RuvBL1/RuvBL2 bound to SPAG1 C-ter -

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Basic information

Entry
Database: EMDB / ID: EMD-52013
TitleHexameric RuvBL1/RuvBL2 bound to SPAG1 C-ter
Map data
Sample
  • Complex: Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1
    • Complex: Components that form the hexameric Ring
      • Protein or peptide: RuvB-like 1
      • Protein or peptide: RuvB-like 2
    • Protein or peptide: Sperm-associated antigen 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ ATPase / R2SP Complex / R2TP-Like complex / PAQosome / Molecular Motor / CHAPERONE
Function / homology
Function and homology information


axonemal dynein complex assembly / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex ...axonemal dynein complex assembly / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / Ino80 complex / regulation of double-strand break repair / box C/D snoRNP assembly / protein folding chaperone complex / regulation of chromosome organization / NuA4 histone acetyltransferase complex / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / Deposition of new CENPA-containing nucleosomes at the centromere / telomere maintenance / DNA helicase activity / TBP-class protein binding / positive regulation of DNA repair / cellular response to estradiol stimulus / euchromatin / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / ADP binding / beta-catenin binding / DNA Damage Recognition in GG-NER / chromatin DNA binding / nuclear matrix / cellular response to UV / UCH proteinases / transcription corepressor activity / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / nucleosome / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / hydrolase activity / protein stabilization / nuclear speck / cilium / ciliary basal body / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribonucleoprotein complex / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / GTP binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / 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 / Tetratricopeptide repeat ...: / 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 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Sperm-associated antigen 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsSanto PE / Plisson-Chastang C
Funding support France, Portugal, 7 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)ANR-16-CE11-0032-04 France
Centre National de la Recherche Scientifique (CNRS)ANR-23-CE12-0022 YMCR France
Centre National de la Recherche Scientifique (CNRS)ANR-23-CE44-0035 NAProt-XLMS France
Fundacao para a Ciencia e a TecnologiaUIDB/04462/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04462/2020 Portugal
Other governmentProFI - ANR-10-INBS-08-03
Other governmentLS4FUTURE - LA/P/0087/2020
CitationJournal: To Be Published
Title: R2TP-like complexes as quaternary chaperones. A comprehensive overview to understand the dynamic R2SP complex
Authors: Santo PE / Chago ME / Ley M / Gizardin-Fredon H / Chenuel T / Desligniere E / Plassart L / Paiva ACF / Sousa PMF / Bertrand E / Charpentier B / Verheggen C / Quinternet M / Meyer P / ...Authors: Santo PE / Chago ME / Ley M / Gizardin-Fredon H / Chenuel T / Desligniere E / Plassart L / Paiva ACF / Sousa PMF / Bertrand E / Charpentier B / Verheggen C / Quinternet M / Meyer P / Bandeiras TM / Cianferani S / Plisson-Chastang C / Manival X
History
DepositionNov 5, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52013.png

Downloads & links

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Map

FileDownload / File: emd_52013.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 304 pix.
= 196.08 Å		0.65 Å/pix.
x 304 pix.
= 196.08 Å		0.65 Å/pix.
x 304 pix.
= 196.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00458
Minimum - Maximum-0.021228906 - 0.033475775
Average (Standard dev.)0.000098942204 (±0.0014339341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 196.07999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52013_msk_1.map
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Additional map: #1

Fileemd_52013_additional_1.map
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Additional map: Phenix Sharpened Half1-Map with Model-based Anisotropic Sharpening

Fileemd_52013_additional_2.map
AnnotationPhenix Sharpened Half1-Map with Model-based Anisotropic Sharpening
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Additional map: Phenix Sharpened Half2-Map with Model-based Anisotropic Sharpening

Fileemd_52013_additional_3.map
AnnotationPhenix Sharpened Half2-Map with Model-based Anisotropic Sharpening
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Additional map: Phenix Sharpened PostProcess Map with Model-based Anisotropic Sharpening...

Fileemd_52013_additional_4.map
AnnotationPhenix Sharpened PostProcess Map with Model-based Anisotropic Sharpening
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Half map: #2

Fileemd_52013_half_map_1.map
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Half map: #1

Fileemd_52013_half_map_2.map
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Sample components

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Entire : Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1

EntireName: Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1
Components
  • Complex: Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1
    • Complex: Components that form the hexameric Ring
      • Protein or peptide: RuvB-like 1
      • Protein or peptide: RuvB-like 2
    • Protein or peptide: Sperm-associated antigen 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1

SupramoleculeName: Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Co-expressed RuvBL1/2 complex incubated with co-expressed SPAG1/PIH1D2 complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 338 KDa

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Supramolecule #2: Components that form the hexameric Ring

SupramoleculeName: Components that form the hexameric Ring / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: RuvBL1 (Chains A-C), amino acids 125-235, and RuvBL2 (Chain E), amino acids 133-238, are present in this model, although the final PostProcess map lacks sufficient density. These reagions ...Details: RuvBL1 (Chains A-C), amino acids 125-235, and RuvBL2 (Chain E), amino acids 133-238, are present in this model, although the final PostProcess map lacks sufficient density. These reagions were rigid fitted in the Refine Map (Reference models 2C9O for RuvBL1 and 6H7X for RuvBL2).
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: 3 / 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: 3 / 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: Sperm-associated antigen 1

MacromoleculeName: Sperm-associated antigen 1 / type: protein_or_peptide / ID: 3 / Details: Truncated Construct from 622-926 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.797664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTKDYPSLW GFGTTKTFKI PIEHLDFKYI EKCSDVKHLE KILCVLRSGE EGYYPELTEF CEKHLQALAP ESRALRKDKP AATAASFTA EEWEKIDGDI KSWVSEIKKE EDKMHFHETE TFPAMKDNLP PVRGSNSCLH VGKEKYSKRP TKKKTPRDYA E WDKFDVEK ...String:
MTTKDYPSLW GFGTTKTFKI PIEHLDFKYI EKCSDVKHLE KILCVLRSGE EGYYPELTEF CEKHLQALAP ESRALRKDKP AATAASFTA EEWEKIDGDI KSWVSEIKKE EDKMHFHETE TFPAMKDNLP PVRGSNSCLH VGKEKYSKRP TKKKTPRDYA E WDKFDVEK ECLKIDEDYK EKTVIDKSHL SKIETRIDTA GLTEKEKDFL ATREKEKGNE AFNSGDYEEA VMYYTRSISA LP TVVAYNN RAQAEIKLQN WNSAFQDCEK VLELEPGNVK ALLRRATTYK HQNKLREATE DLSKVLDVEP DNDLAKKTLS EVE RDLKNS EAASETQTKG KRMVIQEIEN SEDEEGKSGR KHEDGGGDKK PAEPAGAARA AQPCVMGNIQ KKLTGKAEGG KRPA RGAPQ RGQTPEAGAD KRSPRRASAA AAAGGGATGH PGGGQGAENP AGLKSQGNEL FRSGQFAEAA GKYSAAIALL EPAGS EIAD DLSILYSNRA ACYLKEGNCS GCIQDCNRAL ELHPFSMKPL LRRAMAYETL EQYGKAYVDY KTVLQIDCGL QLANDS VNR LSRILMELDG PNWREKLSPI PAVPASVPLQ AWHPAKEMIS KQAGDSSSHR QQGITDEKTF KALKEEGNQC VNDKNYK DA LSKYSECLKI NNKECAIYTN RALCYLKLCQ FEEAKQDCDQ ALQLADGNVK AFYRRALAHK GLKNYQKSLI DLNKVILL D PSIIEAKMEL EEVTRLLNLK DKTAPFNKEK ERRKIEIQEV NEGKEEPGRP AGEVSMGCLA SEKGGKSSRS PEDPEKLPI AKPNNAYEFG QIINALSTRK DKEACAHLLA ITAPKDLPMF LSNKLEGDTF LLLIQSLKNN LIEKDPSLVY QHLLYLSKAE RFKMMLTLI SKGQKELIEQ LFEDLSDTPN NHFTLEDIQA LKRQYEL

UniProtKB: Sperm-associated antigen 1

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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

Concentration0.45 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
170.0 mMNaClSodium Cloride
0.5 mMC9H15O6PTCEP
2.0 mMMgCl2Magnesium Chloride

Details: 20 mM HEPES, 170 mM NaCL, 2mM MgCl2, 0.5 mM TCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP
DetailsSample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 16000 / Average electron dose: 51.92 e/Å2 / Details: 40 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 2158039
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 167033
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Avg.num./class: 300000 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial Local fitting was done using chimera, and PHENIX was used for flexible fitting
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 126 / Target criteria: Cross-correlation coefficient
Output model

PDB-9hb4:
Hexameric RuvBL1/RuvBL2 bound to SPAG1 C-ter

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