2024-10-30 REL RCSB RCSB RCSB 2021-10-30 2023-05-10 2023-05-10 2024-10-30 Department of Energy (DOE, United States) DE-AC02-05CH11231 United States National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) R01HL115153 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM104427 United States National Institutes of Health/National Institute of Mental Health (NIH/NIMH) R01MH077303 United States National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) R01DK042667 United States Tertiary structure of an individual particle of self-folding RNA polymer (particle #052) Liu J Ren G Single molecule structure, Individual Particle cryo-Electron Tomography, IPET, Cryo-ET, tertiary structure, Structural Flexibility, Self-folding mechanism, RNA origami, RNA Liu J McRae EKS Zhang M Geary C Andersen ES Ren G Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography. Nat Commun UK 15 9084 9084 2024 39433544 doi:10.1038/s41467-024-52914-1 2041-1723 Liu J McRae EKS Zhang M Geary C Andersen ES Ren G Tertiary structure of single-instant RNA molecule reveals folding landscape. Biorxiv US 2023 37292713 doi:10.1101/2023.05.19.541511 2692-8205 RNA Origami 6 Helix Bundle with Clasp (6HBC) RNA Origami 6 Helix Bundle with Clasp (6HBC) 0 1
The RNA was transcribed from linearized DNA template using T7 RNA polymerase purified in house.
synthetic construct 0.23 RNA Origami 6 Helix Bundle with Clasp (6HBC) synthetic construct GGGAGAGUACUAUUCAGAUGCAGACCGCAAGUUCAGAGCGGUUUGCAUCUAGGGUACGUUUUCGAACGUAUCCUCCGACUAAGUGUAUUCGUAUACUUAGUGCCUUGUGCCUGCUUCGGCAGGCAUGACCCAAAUGUGCCUUUCGGGGCACAUUUCCGGUCAUCCAAGUUCGCUUGGGUGAUGCGGGCGUAUAGGUUCGUCUAUACGUCCGCGUUUUCCGAGAAGAGGUAACUCGGGAAACCGGUCCACGUGACAAAGGUAGAGUUACGUGGAGGGAGCAGCUGCAAAGGGAUAAUGCAGUUGCUGGCUGGAUGCCAGAACUCACGACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAACGUGAGAGGGGUCGGUUCCCCGAGCAUAGACCAAUAUCCCAGGUUUAUGCUCCCCAACGCUGGACGAACUACCUACGUCUAGCGUUCCGGCAAAUGAGUCAAUACCUCAGACUUAUUUGCGGUGCCUGAGCCUAAACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGUUCGCUGGAGCCGACGGUAGCGCUGCGUUCGCGCAGUGCUAGGGAGCAUCCGUUUUCGAGCGGAUGCUGGGCGGUUGCCUGUUCGCAGGCAAUCGGGCCUACUCAUGAUUCGUCAUGAGUGGUGACAGCGUGAUGUUCGCAUUACGCUGUCGGGUAGAUGGAGAAUU tomography particle 0.3 8.0 25.0 HEPES 5.0 MgCl2 100.0 KCl ETHANE 90 277 LEICA EM GP
In vitro transcribed RNA was purified by size exclusion chromatography and spin concentrated in amicon spin columns.
NO SECTIONING FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 BIOQUANTUM (6k x 4k) 1 21 0.88 8.0 1
Motion correction of the multi-frame movie was conducted by MotionCor2. The tilt series of whole micrographs were initial aligned by IMOD. Additionally, to reduce the image noise, tilt series were further conducted by a machine learning, a median-filter process and a contrast enhancement method.
FOURIER SPACE 28.0 FSC 0.5 CUT-OFF
The targeted images of individual particle were reconstructed by Individual-Particle Electron Tomography (IPET). To reduce the missing-wedge artifact caused by the limited tilt angle range, the final 3D map was submitted to a low-tilt tomographic 3D reconstruction method (LoTToR). IPET 3D map was low-pass filtered to 0.8 nm following by Gaussian filtering (standard deviation is 3.0) and median filter (3x3x3) using EMAN and UCSF Chimera, and displayed by Chimera with applied the hidden dust function.
21 emd_25287.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 240.64 240.64 240.64 90.0 90.0 90.0 X Y Z -1.3819947 5.3006506 0.035120662 0.28674832 1.88 1.88 1.88 EMDB