2020-01-29 REL RCSB RCSB RCSB 2016-04-13 2016-07-06 2016-07-06 2020-01-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM115710 United States Methanococcus jannaschii box C/D sRNP Yip WSV Shigematsu H Taylor DW Baserga SJ Yip WS Shigematsu H Taylor DW Baserga SJ Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Res. UK 2016 27342279 doi:10.1093/nar/gkw576 1362-4962 0389 NARHAD EMD-8146 associated EM volume Methanococcus janaschii box C/D sRNP Methanococcus janaschii box C/D sRNP 0 1 2 3 4 Methanocaldococcus jannaschii 0.366 L7Ae Methanocaldococcus jannaschii Escherichia coli LEVO MAVYVKFKVPEEIQKELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDAEELKVLIEKVNVLKQ Nop5 Methanocaldococcus jannaschii Escherichia coli LEVO MIYVTFTPYGAFGVKDNKEVSGLEDIEYKKLFNEEEIPDIMFKLKTQPNKIADELKEEWGDEIKLETLSTEPFNIGEFLRNNLFKVGKELGYFNNYDEFRKKMHYWSTELTKKVIKSYAQQKDKIIIQVAEAISDLDKTLNLLSERLREWYSLYFPELDHLVNKHEVYANLITKLGKRKNFTKSQLKKILPSKLAGKIAEAAKNSMGGELEDYDLDVIVKFAEEINHLYEKRKELYNYLEKLMNEEAPNITKLAGVSLGARLIGLAGGLEKLAKMPASTIQVLGAEKALFAHLRMGVEPPKHGIIYNHPLIQGSPHWQRGKIARALACKLAIAARADYVGDYIADELLEKLNKRVEEIRRKYPKPPK Fibrillarin Methanocaldococcus jannaschii Escherichia coli LEVO MEDIKIKEIFENIYEVDLGDGLKRIATKSIVKGKKVYDEKIIKIGDEEYRIWNPNKSKLAAAIIKGLKVMPIKRDSKILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVMFVGIWEGK Methanococcus jannaschii sR8 box C/D sRNA AAAUCGCCAAUGAUGACGAUUGGCUUUGCUGAGUCUGUGAUGAACCGUAUGAGCACUGAGGCGAUUU singleParticle particle 7.5 20.0 C8H18N2O4S HEPES 300.0 NaCl sodium chloride 1.5 MgCl2 magnesium chloride Electron Microscopy Sciences COPPER 400 CARBON CONTINUOUS PLASMA CLEANING OTHER ETHANE 100 281 FEI VITROBOT MARK III
Blotting time 5 seconds; Blot offset -1 mm; plunged into liquid ethane (FEI VITROBOT MARK III)..
FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 2.5 4.0 29000.0 NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 833 4.25 30.0
Session 1
 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 281 7.25 30.0
Session 2
 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 546 6.25 30.0
Session 3
 1 164282 CTFFIND3 CTFFIND3 was used for CTF estimation. RELION 1.3 CTF was corrected in Relion using the parameters from CTFFIND3.
CTFFIND3 in Relion was used for CTF estimation
 EMD-1636
A Methanococcus jannaschii negatively-stained EM map low-passed to 60 Angstrom resolution was used as the initial model for 3D reconstruction.
 C2 9.0 FSC 0.143 CUT-OFF RELION 1.3 3D auto-refine
3D refinement was performed on "shiny" particles that have beam-induced motions corrected by lm-bfgs alignparts.
32771 PROJECTION MATCHING Reion 1.3 Relion 3D auto-refine
Refinement was performed using Relion 3D auto-refine. Initial angular sampling was 7.5 degrees; initial offset range was 5 pixels; initial offset step was 1 pixel.
 PROJECTION MATCHING RELION 1.3 Relion 3D auto-refine
Refinement was performed using Relion 3D auto-refine. Angular sampling, offset range, and offset step sizes were automatically adjusted in Relion.
 3 24000 RELION 1.3 Relion 3D Classification
3D classification was performed on "shiny" particles that have beam-induced motions corrected by lm-bfgs alignparts.
 emd_8146.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 -144 -144 -144 288 288 288 359.136 359.136 359.136 90.0 90.0 90.0 X Y Z -0.023278335 0.058725648 0.00010509183 0.002525227 1.247 1.247 1.247 0.0159 AUTHOR None 3NVI 2NNW A 8-126 2NNW B RIGID BODY FIT
To perform rigid-body docking, two copies of the co-crystal structure from P. furiosus [PDB ID 3NVI, each containing two copies of L7Ae, kink-turn RNA, and Nop5 lacking the NTD (amino acids 127-373)] were docked as rigid bodies into the center of the EM volume (using "Fit in Map" in Chimera) based on prior knowledge of the location of the Nop5 coiled-coil domain. Subsequently, four copies of P. furiosus Nop5 N-terminal domain (amino acids 8-126) and fibrillarin from PDB ID 2NNW were docked into the four corners of the volume using "Fit to Segments" in Chimera without changing the relative orientation between the two proteins. To refine the docking, a simultaneous multi-fragment docking refinement was performed using Collage in Situs 2.8.
Correlation REAL