Hexameric RuvBL1/RuvBL2 bound to SPAG1 C-ter

2026-04-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2024-11-05 2025-11-19 2025-11-19 2026-04-01 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 Tecnologia UIDB/04462/2020 Portugal Fundacao para a Ciencia e a Tecnologia UIDP/04462/2020 Portugal Other government ProFI - ANR-10-INBS-08-03 Other government LS4FUTURE - LA/P/0087/2020 Hexameric RuvBL1/RuvBL2 bound to SPAG1 C-ter Santo PE Plisson-Chastang C AAA+ ATPase, R2SP Complex, R2TP-Like complex, PAQosome, Molecular Motor, CHAPERONE Santo PE Chagot ME Gizardin-Fredon H Ley M 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 An integrative structural biology approach reveals the dynamic organization of the R2SP quaternary chaperone complex. Nat Commun UK 17 2026 41667496 doi:10.1038/s41467-026-69157-x 2041-1723 9hb4 FULLOVERLAP EMDB EMD-52013 associated EM volume

Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1 Hexameric RuvBL1/RuvBL2 complex bound to C-terminal Reagion of SPAG1 0 1 2 3

Co-expressed RuvBL1/2 complex incubated with co-expressed SPAG1/PIH1D2 complex

Homo sapiens 0.338 Components that form the hexameric Ring 1 1 2

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).

Homo sapiens RuvB-like 1 Homo sapiens 0.050296914 3 Escherichia coli LEVO MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALA LAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIG LKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALE SSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTK TTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK Q9Y265 3.6.4.12 RuvB-like 2 Homo sapiens 0.051222464999999995 3 Escherichia coli LEVO MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPG TGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGK LTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDM APVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLR YAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS Q9Y230 3.6.4.12 Sperm-associated antigen 1 Homo sapiens 0.103797664

Truncated Construct from 622-926

2 Escherichia coli LEVO MTTKDYPSLWGFGTTKTFKIPIEHLDFKYIEKCSDVKHLEKILCVLRSGEEGYYPELTEFCEKHLQALAPESRALRKDKP AATAASFTAEEWEKIDGDIKSWVSEIKKEEDKMHFHETETFPAMKDNLPPVRGSNSCLHVGKEKYSKRPTKKKTPRDYAE WDKFDVEKECLKIDEDYKEKTVIDKSHLSKIETRIDTAGLTEKEKDFLATREKEKGNEAFNSGDYEEAVMYYTRSISALP TVVAYNNRAQAEIKLQNWNSAFQDCEKVLELEPGNVKALLRRATTYKHQNKLREATEDLSKVLDVEPDNDLAKKTLSEVE RDLKNSEAASETQTKGKRMVIQEIENSEDEEGKSGRKHEDGGGDKKPAEPAGAARAAQPCVMGNIQKKLTGKAEGGKRPA RGAPQRGQTPEAGADKRSPRRASAAAAAGGGATGHPGGGQGAENPAGLKSQGNELFRSGQFAEAAGKYSAAIALLEPAGS EIADDLSILYSNRAACYLKEGNCSGCIQDCNRALELHPFSMKPLLRRAMAYETLEQYGKAYVDYKTVLQIDCGLQLANDS VNRLSRILMELDGPNWREKLSPIPAVPASVPLQAWHPAKEMISKQAGDSSSHRQQGITDEKTFKALKEEGNQCVNDKNYK DALSKYSECLKINNKECAIYTNRALCYLKLCQFEEAKQDCDQALQLADGNVKAFYRRALAHKGLKNYQKSLIDLNKVILL DPSIIEAKMELEEVTRLLNLKDKTAPFNKEKERRKIEIQEVNEGKEEPGRPAGEVSMGCLASEKGGKSSRSPEDPEKLPI AKPNNAYEFGQIINALSTRKDKEACAHLLAITAPKDLPMFLSNKLEGDTFLLLIQSLKNNLIEKDPSLVYQHLLYLSKAE RFKMMLTLISKGQKELIEQLFEDLSDTPNNHFTLEDIQALKRQYEL Q07617 ADENOSINE-5'-DIPHOSPHATE 0.000427201 6 ADP singleParticle particle 0.45 8.0 20.0 C8H18N2O4S HEPES 170.0 NaCl Sodium Cloride 0.5 C9H15O6P TCEP 2.0 MgCl2 Magnesium Chloride

20 mM HEPES, 170 mM NaCL, 2mM MgCl2, 0.5 mM TCEP

Quantifoil R2/1 COPPER 300 CARBON HOLEY 1.0 GLOW DISCHARGE AIR ETHANE 95 292 LEICA EM GP

Sample was monodisperse

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.9 2.0 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 16000 51.92

40 frames

1 2158039 Gctf PHASE FLIPPING AND AMPLITUDE CORRECTION 1 C1 3.56 FSC 0.143 CUT-OFF RELION 3.0 167033 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 5 300000.0 RELION 3.0 emd_52013.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 X Y Z -0.021228906 0.033475775 0.000098942204 0.0014339341 0.645 0.645 0.645 0.00458 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: RIGID BODY FIT

Initial Local fitting was done using chimera, and PHENIX was used for flexible fitting

Cross-correlation coefficient REAL 126.0 emd_52013_msk_1.map emd_52013_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 Z Y X -0.013584239 0.02353863 0.000025812327 0.0010276705 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: Phenix Sharpened PostProcess Map with Model-based Anisotropic Sharpening emd_52013_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 Z Y X -0.006203684 0.010044569 0.000025790123 0.0006201889 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: Phenix Sharpened Half2-Map with Model-based Anisotropic Sharpening emd_52013_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 X Y Z -0.0027539027 0.008725446 0.00009894429 0.00057251373 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: Phenix Sharpened Half1-Map with Model-based Anisotropic Sharpening emd_52013_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 Z Y X -0.00618939 0.010257963 0.000025834532 0.00062198995 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: emd_52013_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 X Y Z -0.009482357 0.014210331 0.00009902732 0.0009986293 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013:::: emd_52013_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 196.07999 196.07999 196.07999 90.0 90.0 90.0 X Y Z -0.009377128 0.015110911 0.00009885709 0.0009962778 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-52013::::