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 homodimer bound to RNA (substrate 1) 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 7s7b FULLOVERLAP human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex 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,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 2 Escherichia coli LEVO SGDEADRTLFVGNLETKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIKIQ FRS Q9Y580 RNA (46-MER) synthetic construct 0.014605817999999998
The actual RNA sequence is: ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(2PU)ACAAAAAAAA. (2PU) is represented by "N" (any nucleotide. This residue is missing in the coordinates and the chemical is an internal 2' pyrene modified uridine
2 ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(N)ACAAAAAAAA ZINC ION 6.5409e-05 2 ZN singleParticle particle 8 8.0
20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630
 UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE 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 67.6 1
Ab initio model from cryosparc
 4.06 FSC 0.143 CUT-OFF RELION
A total of 618,412 particles were used for the consensus reconstruction with an overall resolution of 4.06 Angstrom (FSC 0.143 cut off). Focused 3D classification and local refinement were performed in several regions of the complex. A composite map was generated using focused reconstructions of ZCCHC8 HD/KID-MTR4 KOW (3.26 Angstrom, FSC = 0.143; 117,561 particles), protomer A MTR4 (3.42 Angstrom, FSC = 0.143; 225,213 particles), protomer B MTR4 (3.54 Angstrom, FSC = 0.143; 236,602 particles), protomer A MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.06 Angstrom, FSC = 0.143; 44,800 particles), and protomer B MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.4 Angstrom, FSC = 0.143 37,088 particles).
618412 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_24882.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 Z Y X -58.578938000000001 117.664664999999999 -0.008782573 1.2400491 1.088 1.088 1.088 11.5 AUTHOR human NEXT dimer bound to RNA - composite structure emd_24882_additional_18.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.040479094 0.052114945 -0.00004603116 0.002241637 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 half map 2 emd_24882_additional_17.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03340936 0.04847288 0.0000067829496 0.00068843743 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 (component map of composite structure) emd_24882_additional_16.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.036481496 0.06566803 -0.000040798936 0.0026041146 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 half map 2 emd_24882_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.010799741 0.031142313 -0.000006260099 0.0013115421 1.088 1.088 1.088 AUTHOR Overall reconstruction half map 2 emd_24882_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03974556 0.047974847 -0.00004558283 0.0022406622 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 half map 1 emd_24882_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.011037214 0.029970989 -0.000006250029 0.001315648 1.088 1.088 1.088 AUTHOR Overall reconstruction half map 1 emd_24882_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03624124 0.07789842 -0.00004039573 0.0018778975 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 half map 1 emd_24882_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.04382355 0.10593177 -0.0000058787555 0.0020743918 1.088 1.088 1.088 AUTHOR focused refinement on ZCCHC8-HD/KID MTR4-KOW half map 2 emd_24882_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.04382355 0.10593177 -0.0000058787555 0.0020743918 1.088 1.088 1.088 AUTHOR focused refinement on ZCCHC8-HD/KID MTR4-KOW half map 1 emd_24882_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.108861625 0.17424564 0.000034363708 0.0011702693 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 (component map of composite structure) emd_24882_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.024659036 0.05646511 0.00008377891 0.0010390388 1.088 1.088 1.088 AUTHOR Overall reconstruction (component map of composite structure) emd_24882_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.037205126 0.07202386 -0.000045664543 0.0016272013 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 half map 2 emd_24882_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.034576133 0.07811188 -0.000040299707 0.0018873924 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 half map 2 emd_24882_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03771441 0.0762739 -0.000045373465 0.0016195986 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 half map 1 emd_24882_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03800157 0.072147615 0.000035599995 0.000988754 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 (component map of composite structure) emd_24882_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.122267574 0.21120737 0.00002201352 0.0015595967 1.088 1.088 1.088 AUTHOR focused refinement on ZCCHC8-HD/KID MTR4-KOW (component map of composite structure) emd_24882_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.13280539 0.1854997 0.000008391287 0.001104027 1.088 1.088 1.088 AUTHOR focused refinement on protomer B MTR4 (component map of composite structure) emd_24882_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 417.79202 417.79202 417.79202 90.0 90.0 90.0 X Y Z -0.03682425 0.059457853 -0.00004136386 0.0025229417 1.088 1.088 1.088 AUTHOR focused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 half map 1