Symmetry-expanded reconstruction of augmin T-II bonsai on the microtubule

2025-11-12 REL RCSB 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.journal_volume _citation.page_first _citation.page_last _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 RCSB RCSB 2024-08-08 2025-08-13 2025-08-13 2025-11-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) F32 GM142149 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) K99 GM152794 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01 GM138854 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01 GM141100 United States Symmetry-expanded reconstruction of augmin T-II bonsai on the microtubule Travis SM Zhang R Microtubule, augmin, CH, spindle, CELL CYCLE Travis SM Kraus J McManus CT Golden K Zhang R Petry S How augmin establishes the angle of the microtubule branch site. Nat Commun UK 16 9646 9646 2025 41173848 doi:10.1038/s41467-025-64650-1 2041-1723 9d2b FULLOVERLAP EMDB EMD-46489 associated EM volume

Augmin T-II bonsai on the microtubule Augmin T-II bonsai on the microtubule 0 1 2 3 4 5

Complex of augmin bound to the microtubule

0.092 GMPCPP microtubule 1 1 2

bovine tubulin polymerized in the presence of GMPCPP

Bos taurus BRAIN augmin T-II bonsai 1 3 4 5

trimeric fragment of Xenopus laevis augmin

Xenopus laevis Tubulin alpha-1B chain Bos taurus BRAIN 0.050204445 2 LEVO MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY P81947 Tubulin beta-2B chain Bos taurus BRAIN 0.049999887 1 LEVO MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA Q6B856 HAUS augmin like complex subunit 6 L homeolog isoform X1 Xenopus laevis 0.033562742 1 Escherichia coli BL21 LEVO MGSSHHHHHHSGRENLYFQGSMQSGSRPHLAWQREHMWLALQGLGFESGAEAANAGKTLVHVTFGVNMFDKPNKDAFYVV FHFLFGKLDNVRCKEVFRYCWPPLDKKRDAEFRKACCEWLKKISDEVGAGFPQVVASIFLSPGGPKFVHLLYHFARYVML QHIKRDADAGNVFISEALQSKIQDPQKALARNKLARQKYLKVLQKENLVIEEYQRKAQLLIKQIRDMRSEHVALQNQQKL AEKVDRKISDKDENIQKTRCMWNTIMQMLKEMEKEVDVVDAVVRGNIDQ A0A8J1MAE8 HAUS augmin like complex subunit 7 S homeolog Xenopus laevis 0.031848111 1 Escherichia coli BL21 LEVO MADPWSHPQFEKGGTGGKELGAAVELYERLQMLSCPCLEGVYLTDPQSIYELLCTPSSHRLDILQWLCSRIYPPVQEQLS SLKESQTDTKVKEIAKLCFDLMLCHFDDLDLIRGHASPFKQISFIGQLLDVIQYPDTISSNVILESLSHSTEKNVVTCIR ENEELLKELFSSPHFQATLSPECNPWPADFKPLLNAEESLQKRATQSSKGKDMSNSVEALLEISSSLKALKEECVDLCSS VTDGDKVIQSLRLALTDFHQLTIAFNQIYANEFQWSHPQFEK B1H1T5 HAUS augmin-like complex subunit 8 Xenopus laevis 0.028742901999999997 1 Escherichia coli BL21 LEVO MRSMSEAGVAPIEDGSQNSSGGSSGDAALKKSKGGAKVVKSRYMQIGRSKVSKNSLANTTVCSGGKVPERGSGGTPTRRS LAPHKAKITAAVPLPALDGSIFTKEDLQSTLLDGHRIARPDLDLSVINDRTLQKITPRPVVTSEQKKPKRDTTPVNLVPE DMVEMIESQTLLLTYLTIKMQKNLFRLEEKAERNLLLVNDQKDQLQETIHMMKRDLTLLQREERLRDLIEKQDEVLTPVV TSKDPFKDNYTTFATALDST Q0IHJ3 GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 2 GTP MAGNESIUM ION 2.4305e-05 3 MG PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER 0.0005212079999999999 1 G2P singleParticle filament 6.8 0.08 PIPES 1.0 EGTA 1.0 MgCl2 magnesium chloride 0.05 Tween-20 Quantifoil R1.2/1.3 COPPER 400 CARBON HOLEY 10.0 GLOW DISCHARGE 60 AIR 0.037 ETHANE 85 298 LEICA EM GP

20 uM tubulin, 10 uM augmin T-II bonsai

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 0.1 2.0 3.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER FEI FALCON III (4k x 4k) COUNTING 4096 4096 1 2088 4.1 15.0 1 177242 CTFFIND PHASE FLIPPING AND AMPLITUDE CORRECTION

Both 13-protofilament and 14-protofilament reference models were given, as detailed in Valdez et al 2023 DOI: 10.1101/2023.12.18.571906

1 C1 3.08 FSC 0.143 CUT-OFF cryoSPARC 1772567 NOT APPLICABLE cryoSPARC cryoSPARC heterogeneous refinement was used to assign initial angles NOT APPLICABLE FREALIGN 13 FREALIGN was used for seam search emd_46489.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 406 406 406 0 0 0 406 406 406 570.836 570.836 570.836 90.0 90.0 90.0 X Y Z -0.74149936 1.4458637 0.002991524 0.032906726 1.406 1.406 1.406 0.121 AUTHOR ::::EMDATABANK.org::::EMD-46489:::: 6DPU A PDB experimental model 6DPU B PDB experimental model 8FCK F PDB experimental model 8FCK G PDB experimental model 8FCK H PDB experimental model FLEXIBLE FIT REAL 36.829999999999998 emd_46489_msk_1.map emd_46489_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 406 406 406 0 0 0 406 406 406 570.836 570.836 570.836 90.0 90.0 90.0 X Y Z -0.33437884 1.4808015 0.00016631473 0.009415183 1.406 1.406 1.406 AUTHOR ::::EMDATABANK.org::::EMD-46489:::: Sharpened map emd_46489_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 406 406 406 0 0 0 406 406 406 570.836 570.836 570.836 90.0 90.0 90.0 X Y Z -0.91569144 1.6170098 -0.0001614319 0.041042183 1.406 1.406 1.406 AUTHOR ::::EMDATABANK.org::::EMD-46489:::: emd_46489_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 406 406 406 0 0 0 406 406 406 570.836 570.836 570.836 90.0 90.0 90.0 X Y Z -0.91224796 1.6293732 -0.00017056987 0.04107297 1.406 1.406 1.406 AUTHOR ::::EMDATABANK.org::::EMD-46489::::