2024-06-05 REL RCSB RCSB RCSB 2021-09-15 2022-06-15 2022-06-15 2024-06-05 Howard Hughes Medical Institute (HHMI) United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM118080 United States Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) Puno MR Lima CD Helicase, ATPase, RNA, Exosome, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex Puno MR Lima CD Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Cell 185 2132 2147.e26 2022 35688134 doi:10.1016/j.cell.2022.04.016 1097-4172 7s7c FULLOVERLAP human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) 0 1 2 3 4 Homo sapiens Exosome RNA helicase MTR4 Homo sapiens 0.11822496099999999 2 Escherichia coli LEVO SGDMADAFGDELFSVFEGDSTTAAGTKKDKEKDKGKWKGPPGSADKAGKRFDGKLQSESTNNGKNKRDVDFEGTDEPIFG KKPRIEESITEDLSLADLMPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSV LVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLY RGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQ HYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDLAKGDQKGRKGGTKGPSNVFKIVKMIMERNFQPVIIFSFSKK DCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIK ALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSAD PLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLG KEIEEYIHKPKYCLPFLQPGRLVKVKNEGDDFGWGVVVNFSKKSNVKPNSGELDPLYVVEVLLRCSKESLKNSATEAAKP AKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKV EAFEHRMYSHPLHNDPNLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVA CEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEET YLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFA ASLYL P42285 3.6.4.13 Zinc finger CCHC domain-containing protein 8 Homo sapiens 0.069259805 2 Escherichia coli LEVO SGDMAAEVYFGDLELFEPFDHPEESIPKPVHTRFKDDDGDEEDENGVGDAELRERLRQCEETIEQLRAENQELKRKLNIL TRPSGILVNDTKLDGPILQILFMNNAISKQYHQEIEEFVSNLVKRFEEQQKNDVEKTSFNLLPQPSSIVLEEDHKVEESC AIKNNKEAFSVVGSVLYFTNFCLDKLGQPLLNENPQLSEGWEIPKYHQVFSHIVSLEGQEIQVKAKRPKPHCFNCGSEEH QMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRYHAEEVEERFGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLG YPPGWLKEAELENSGLALYDGKDGTDGETEVGEIQQNKSVTYDLSKLVNYPGFNISTPRGIPDEWRIFGSIPMQACQQKD VFANYLTSNFQAPGVKSGGAVDEDALTLEELEEQQRRIWAALEQAESVNSDSDVPVDTPLTGNSVASSPCPNELDLPVPE GKTSEKQTLDEPEVPEIFTKKSEAGHASSPDSEVTSLCQKEKAELAPVNTEGALLDNGSVVPNCDISNGGSQKLFPADTS PSTATKIHSPIPDMSKFATGITPFEFENMAESTGMYLRIRSLLKNSPRNQQKNKKASE Q6NZY4 Q6NZY4 RNA-binding protein 7 Homo sapiens 0.009462986 1 Escherichia coli LEVO SGDEADRTLFVGNLETKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIKIQ FRS Q9Y580 RNA (30-MER) synthetic construct 0.009017486 2 GGCGCGCGCCAAAAAUUUUUAAAAAAAA ZINC ION 6.5409e-05 1 ZN singleParticle particle 8.0 ETHANE 100 295 FEI VITROBOT MARK IV
30 s wait time, blot for 2.5 s before plunging.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 77.5
Dataset 1
 GATAN K3 (6k x 4k) 66.0
Datasets 2 and 3
 2
3 datasets collected using Gatan K2 Summit and Gatan K3 image detectors were used for the reconstructions.
Ab initio model from cryosparc
 3.62 FSC 0.143 CUT-OFF RELION
A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map with focused refinement maps of MTR4 core (3.5 Angstrom FSC=0.143), MTR4 core-ZCCHC8 PSP-RBM7-RNA (3.42 Angstrom, FSC=0.143), RBM7-RNA (3.94 Angstrom, FSC=0.143), MTR4-ZCCHC8 HD/KID (3.62 Angstrom, FSC=0.143), and MTR4 KOW-ZCCHC8 HD/KID (3.34 Angstrom, FSC=0.143) regions.
252638 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_24883.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 Z Y X -43.078094 72.188469999999995 0.001339072 1.0651523 1.1 1.1 1.1 8.0 AUTHOR NEXT-RNA subtrate 2 complex - composite reconstruction emd_24883_additional_18.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.024712801 0.05803428 0.0000404566 0.0017802658 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - half map 2 emd_24883_additional_17.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.026171215 0.07214391 0.00003823643 0.0014775265 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 KOW-ZCCHC8 HD/KID region - half map 1 emd_24883_additional_16.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.022834156 0.062809154 0.000040392166 0.0018518175 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4-ZCCHC8 HD/KID - half map 2 emd_24883_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.023317352 0.058166754 0.000038972372 0.001857041 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4-ZCCHC8 HD/KID - half map 1 emd_24883_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.022757292 0.06804658 0.00003849227 0.0017570108 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core - half map 1 emd_24883_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.020794356 0.05587802 0.000038741626 0.00133514 1.1 1.1 1.1 AUTHOR focused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 1 emd_24883_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.023571998 0.073598094 0.000039737304 0.0017581322 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core - half map 2 emd_24883_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.018835207 0.05313875 0.000041035786 0.001830402 1.1 1.1 1.1 AUTHOR overall reconstruction half map emd_24883_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.022422887 0.054741986 0.00004067008 0.0013377406 1.1 1.1 1.1 AUTHOR focused refinement map of RBM7-ZCCHC8 middle region-RNA - half map 2 emd_24883_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.025849616 0.070221804 0.000039863902 0.0014783732 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 KOW-ZCCHC8 HD/KID - half map 2 emd_24883_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.028870266 0.059797555 0.000038793107 0.0017839863 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - half map 1 emd_24883_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.021537779 0.053495917 0.0000394218 0.0018334974 1.1 1.1 1.1 AUTHOR overall reconstruction half map 1 emd_24883_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.16696456 0.26496732 0.00005182464 0.0025528246 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 KOW-ZCCHC8 HD/KID - component of composite reconstruction emd_24883_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.10076038 0.16450007 0.00011654666 0.002489671 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4-ZCCHC8 HD/KID - component of composite reconstruction emd_24883_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.07921705 0.13395748 0.000051967403 0.0012881946 1.1 1.1 1.1 AUTHOR focused refinement map of RBM7-ZCCHC8 middle region-RNA - component of composite reconstruction emd_24883_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.08837431 0.14567645 0.00007986683 0.0018289107 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core-ZCCHC8 middle region-RBM7-RNA - component of composite reconstruction emd_24883_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.10786265 0.15937339 0.00009007657 0.0026045728 1.1 1.1 1.1 AUTHOR focused refinement map of MTR4 core - component of composite reconstruction emd_24883_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 308.0 308.0 308.0 90.0 90.0 90.0 X Y Z -0.09731507 0.14800212 0.00014933822 0.0025209 1.1 1.1 1.1 AUTHOR overall map