2025-12-17 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2025-07-20 2025-11-12 2025-11-12 2025-12-17 National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) 1ZIAHL006264 United States In situ microtubule of EpoB-induced regenerating axons Bodakuntla S Taira K Yamada Y Alvarez-Brecht P Cada AK Basnet N Zhang R Martinez-Sanchez A Biertumpfel C Mizuno N cytoskeleton, microtubules, neuroregeneration, axon, STRUCTURAL PROTEIN Bodakuntla S Taira K Yamada Y Alvarez-Brecht P Cada AK Basnet N Zhang R Martinez-Sanchez A Biertumpfel C Mizuno N In situ structural mechanism of epothilone-B-induced CNS axon regeneration. Nature UK 648 477 487 2025 41224993 doi:10.1038/s41586-025-09654-z 1476-4687 0006 NATUAS EMD-71751 other EM volume
Cryo-ET reconstruction of an axon
 EMD-71752 other EM volume
Cryo-ET reconstruction of a regenerating axon after axotomy showing branching microtubules
 EMD-71753 other EM volume
Cryo-ET reconstruction of a regenerating axon after axotomy showing polymerizing microtubules
 EMD-71754 other EM volume
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy
 EMD-71755 other EM volume
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy
 9pnd FULLOVERLAP EMDB EMD-71751 other EM volume
Cryo-ET reconstruction of an axon
 EMDB EMD-71752 other EM volume
Cryo-ET reconstruction of a regenerating axon after axotomy showing branching microtubules
 EMDB EMD-71753 other EM volume
Cryo-ET reconstruction of a regenerating axon after axotomy showing polymerizing microtubules
 EMDB EMD-71754 other EM volume
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy
 EMDB EMD-71755 other EM volume
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy
 EMDB EMD-71750 associated EM volume
In situ microtubule of EpoB-induced regenerating axons
 Microtubule, axonal Microtubule, axonal 0 1 2
from Epothilone B-induced regenerating explant axons from thalamus primary mouse embryo tissue after axotomy
Mus musculus Brain Thalamus Axon Tubulin beta-3 chain Mus musculus Brain Thalamus 0.050467491999999996
TUBB3 component of microtubules
2 LEVO MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGA FGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGR MSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEMYEDDDEESEAQGPK Q9ERD7 Detyrosinated tubulin alpha-1A chain Mus musculus Brain Thalamus 0.05018844099999999
TUBA1A component of microtubules
2 LEVO MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY P68369 MAGNESIUM ION 2.4305e-05 4 MG GUANOSINE-5'-DIPHOSPHATE 0.000443201 2 GDP 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE 0.000507683 2 EPB GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 2 GTP water 1.8015e-05 4 HOH helical filament 7.2
Gibco Neurobasal Media
 Quantifoil R1/4 GOLD 200 SILICON DIOXIDE HOLEY GLOW DISCHARGE AIR 3.8000000000000003
coated with poly-L-lysine and laminin
 ETHANE 95 298 FEI VITROBOT MARK IV
induced by axotomy in the presence of 1 nM Epothilone B
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum GATAN K3 BIOQUANTUM (6k x 4k) 11520 8184 5 4034 54.0
curated image number
 1 1 9.695 -27.64 C1 FOURIER SPACE 3.19 FSC 0.143 CUT-OFF cryoSPARC 4.5 118551 cryoSPARC 4.5 PHASE FLIPPING AND AMPLITUDE CORRECTION 399396 cryoSPARC 4.5
picked in filament tracer with overlapping boxes with a step size of 82.5 Angstrom
 MAXIMUM LIKELIHOOD cryoSPARC 4.5
seam detection in frealign 9.11
 emd_71750.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 549.5 549.5 549.5 90.0 90.0 90.0 X Y Z -1.1436235 2.643172 0.0050454377 0.10371101 1.37375 1.37375 1.37375 0.5 AUTHOR sharpened map from local refinement 6dpu PDB experimental model FLEXIBLE FIT REAL emd_71750_msk_1.map emd_71750_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 549.5 549.5 549.5 90.0 90.0 90.0 X Y Z -0.5726752 1.718884 0.0050454377 0.08709368 1.37375 1.37375 1.37375 AUTHOR map from local refinement emd_71750_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 549.5 549.5 549.5 90.0 90.0 90.0 X Y Z -0.9062939 2.0189898 0.0017082359 0.14213303 1.37375 1.37375 1.37375 AUTHOR half map from local refinement emd_71750_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 549.5 549.5 549.5 90.0 90.0 90.0 X Y Z -0.93904066 1.9787736 0.0017030131 0.14207037 1.37375 1.37375 1.37375 AUTHOR half map from local refinement