2024-06-05 REL RCSB RCSB RCSB 2022-01-12 2022-12-28 2022-12-28 2024-06-05 Other private ASAP-000519 United States Michael J. Fox Foundation 18321 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM121772 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM107214 United States Structure of Leucine Rich Repeat Kinase 2's ROC domain interacting with the microtubule facing the plus end Matyszewski M Leschziner AE parkinson's disease, microtubule, kinase, gtpase, CYTOSOLIC PROTEIN Snead DM Matyszewski M Dickey AM Lin YX Leschziner AE Reck-Peterson SL Structural basis for Parkinson's disease-linked LRRK2's binding to microtubules. Nat.Struct.Mol.Biol. US 29 1196 1207 2022 36510024 doi:10.1038/s41594-022-00863-y 1545-9985 EMD-25649 other EM volume
Original Helical Reconstruction
 EMD-25658 other EM volume
Local refinement focusing both on LRRK2 and the microtubule
 EMD-25897 other EM volume
Local refinement focusing only on a monomer of LRRK2
 7thz FULLOVERLAP LRRK2RCKW filament bound to a 11-pf microtubule with MLi-2 present LRRK2RCKW filament bound to a 11-pf microtubule with MLi-2 present 0 1 Leucine-rich repeat serine/threonine-protein kinase 2 Homo sapiens 0.022191761999999997 1 Spodoptera frugiperda LEVO YNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQ RALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNAT EESDALAKLRKTIINESLNFKIRDQLVVGQLIPD Q5S007 2.7.11.1 GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP singleParticle filament 7.4 20.0 HEPES 80.0 NaCl Sodium Chloride 0.5 TCEP 2.5 MgCl2 Magnesium Chloride 20.0 GDP
This is the final dilution buffer. The incubation buffer consisted of 1x BRB80, 10% glycerol, 1mM DTT, 1mM GTP, 1mM MgCl2, 10 uM taxol, and 5 uM MLi-2. Sample was diluted 3-fold right before freezing with the final buffer.
 Homemade COPPER 300 CARBON LACEY GLOW DISCHARGE
EMS LC-300 lacey grid used (not homemade, but can't choose EMS as the manufacturer)
 ETHANE 100 277
4.5 uM of LRRK2RCKW (I2020T) was allowed to incubate with 2.25 uM of tubulin dimer, causing both to co-polymerize. 5 uM of MLi-2 was present as well. The sample was diluted 3-fold right before freezing (1.5 uM LRRK2RCKW concentration final).
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 1.5 1.5 36000.0 NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 2 10.0 55.0
250 ms frames
 1 557577
Filament Autopicker with templates created by manual picking. This is before symmetry expansion.
Featureless cylinder for the original helical reconstruction, then subunit from the helical reconstruction after reboxing and symmetry expansion.
 C1 5.0 FSC 0.143 CUT-OFF cryoSPARC 3.2 local refinement, with non-uniform refinement turned off 99854 NOT APPLICABLE NOT APPLICABLE emd_25907.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 348.0 348.0 348.0 90.0 90.0 90.0 X Y Z -1.1120619 2.7757661 0.0058422643 0.059319537 1.16 1.16 1.16 0.254 AUTHOR Sharpened map FLEXIBLE FIT
Used AlphaFold model as initial model (Q5S007) using only the ROC domain. TUB1 was added to the initial refinement to prevent ROC model from entering density reserved for the microtubule. TUB1 was discarded after the initial refinement.
 emd_25907_msk_1.map emd_25907_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 348.0 348.0 348.0 90.0 90.0 90.0 X Y Z -0.3277522 1.8182302 0.0058422624 0.050476667 1.16 1.16 1.16 AUTHOR Non-sharpened map emd_25907_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 348.0 348.0 348.0 90.0 90.0 90.0 X Y Z -0.76196164 2.2059605 0.0005469947 0.11411331 1.16 1.16 1.16 AUTHOR Half map 1 emd_25907_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 348.0 348.0 348.0 90.0 90.0 90.0 X Y Z -0.79900336 2.3736644 0.00063301343 0.1140229 1.16 1.16 1.16 AUTHOR Half map 2