2024-06-05 REL PDBj PDBj PDBj 2021-05-15 2021-12-29 2021-12-29 2024-06-05 National Natural Science Foundation of China (NSFC) 31822001 China Fang CL Wu XX DNA-directed RNA polymerase IV, RNA- dependent RNA polymerase 2, RNA-directed DNA methylation pathway, TRANSCRIPTION Huang K Wu XX Fang CL Xu ZG Zhang HW Gao J Zhou CM You LL Gu ZX Mu WH Feng Y Wang JW Zhang Y Science US 374 1579 1586 2021 34941388 doi:10.1126/science.abj9184 1095-9203 0038 SCIEAS 7eu0 FULLOVERLAP A. thaliana Pol IV-RDR2 backtracked complex A. thaliana Pol IV-RDR2 backtracked complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Arabidopsis thaliana 0.55 DNA-directed RNA polymerase IV subunit 1 Arabidopsis thaliana 0.16953528099999998 1 LEVO MEDDCEELQVPVGTLTSIGFSISNNNDRDKMSVLEVEAPNQVTDSRLGLPNPDSVCRTCGSKDRKVCEGHFGVINFAYSI INPYFLKEVAALLNKICPGCKYIRKKQFQITEDQPERCRYCTLNTGYPLMKFRVTTKEVFRRSGIVVEVNEESLMKLKKR GVLTLPPDYWSFLPQDSNIDESCLKPTRRIITHAQVYALLLGIDQRLIKKDIPMFNSLGLTSFPVTPNGYRVTEIVHQFN GARLIFDERTRIYKKLVGFEGNTLELSSRVMECMQYSRLFSETVSSSKDSANPYQKKSDTPKLCGLRFMKDVLLGKRSDH TFRTVVVGDPSLKLNEIGIPESIAKRLQVSEHLNQCNKERLVTSFVPTLLDNKEMHVRRGDRLVAIQVNDLQTGDKIFRS LMDGDTVLMNRPPSIHQHSLIAMTVRILPTTSVVSLNPICCLPFRGDFDGDCLHGYVPQSIQAKVELDELVALDKQLINR QNGRNLLSLGQDSLTAAYLVNVEKNCYLNRAQMQQLQMYCPFQLPPPAIIKASPSSTEPQWTGMQLFGMLFPPGFDYTYP LNNVVVSNGELLSFSEGSAWLRDGEGNFIERLLKHDKGKVLDIIYSAQEMLSQWLLMRGLSVSLADLYLSSDLQSRKNLT EEISYGLREAEQVCNKQQLMVESWRDFLAVNGEDKEEDSVSDLARFCYERQKSATLSELAVSAFKDAYRDVQALAYRYGD QSNSFLIMSKAGSKGNIGKLVQHSMCIGLQNSAVSLSFGFPRELTCAAWNDPNSPLRGAKGKDSTTTESYVPYGVIENSF LTGLNPLESFVHSVTSRDSSFSGNADLPGTLSRRLMFFMRDIYAAYDGTVRNSFGNQLVQFTYETDGPVEDITGEALGSL SACALSEAAYSALDQPISLLETSPLLNLKNVLECGSKKGQREQTMSLYLSEYLSKKKHGFEYGSLEIKNHLEKLSFSEIV STSMIIFSPSSNTKVPLSPWVCHFHISEKVLKRKQLSAESVVSSLNEQYKSRNRELKLDIVDLDIQNTNHCSSDDQAMKD DNVCITVTVVEASKHSVLELDAIRLVLIPFLLDSPVKGDQGIKKVNILWTDRPKAPKRNGNHLAGELYLKVTMYGDRGKR NCWTALLETCLPIMDMIDWGRSHPDNIRQCCSVYGIDAGRSIFVANLESAVSDTGKEILREHLLLVADSLSVTGEFVALN AKGWSKQRQVESTPAPFTQACFSSPSQCFLKAAKEGVRDDLQGSIDALAWGKVPGFGTGDQFEIIISPKVHGFTTPVDVY DLLSSTKTMRRTNSAPKSDKATVQPFGLLHSAFLKDIKVLDGKGIPMSLLRTIFTWKNIELLSQSLKRILHSYEINELLN ERDEGLVKMVLQLHPNSVEKIGPGVKGIRVAKSKHGDSCCFEVVRIDGTFEDFSYHKCVLGATKIIAPKKMNFYKSKYLK NGTLESGGFSENPGSGSGSDYKDHDGDYKDHDIDYKDDDDKENLYFQGHHHHHHHHHHSSNFPDRSNIWQ DNA-directed RNA polymerases IV and V subunit 2 Arabidopsis thaliana 0.132848047 1 LEVO MPDMDIDVKDLEEFEATTGEINLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEMLVEPSF DVVKKKDNDWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMTYSARIKVNVQVEVFKNTVVKSDKFKTGQDNYVE KKILDVKKQDILIGSIPVMVKSILCKTSEKGKENCKKGDCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWISNSPWTVSFR SENKRNRFIVRLSENEKAEDYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIASIHVADA VCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLFPGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRI ELAGELLEREIRVHLAHARRKMTRAMQKHLSGDGDLKPIEHYLDASVITNGLSRAFSTGAWSHPFRKMERVSGVVANLGR ANPLQTLIDLRRTRQQVLYTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFACGMEEL MDDTCTPLFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVENLQKL KQEKPSQYPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEPKIYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQ KHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMF RSEQIRSYKAEVDAKDSEKRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTER GIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQL LEAALSKGIACPIQKEGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRL VHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIER TPSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGITLNFDTKLC Q9LK40 2.7.7.6 DNA-directed RNA polymerases II, IV and V subunit 3 Arabidopsis thaliana 0.035503218999999996 1 LEVO MDGATYQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSER AMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRDLYSADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRG QELKLRAIARKGIGKDHAKWSPAATVTFMYEPDIIINEDMMDTLSDEEKIDLIESSPTKVFGMDPVTRQVVVVDPEAYTY DEEVIKKAEAMGKPGLIEISPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLDAVRLSDDTVEADDQFGELGAHMRGG Q39211 DNA-directed RNA polymerases II and IV subunit 5A Arabidopsis thaliana 0.024340388999999997 1 LEVO MLTEEELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRNDNSDQLYIFFPDEAKVGVK TMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTV KETQLPRIQVTDPIARYFGLKRGQVVKIIRPSETAGRYVTYRYVV O81098 DNA-directed RNA polymerases II, IV and V subunit 6A Arabidopsis thaliana 0.016670346 1 LEVO MADEDYNDVDDLGYEDEPAEPEIEEGVEEDVEMKENDDVNGEPIEAEDKVETEPVQRPRKTSKFMTKYERARILGTRALQ ISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVEDSWKRQVGGD Q9FJ98 DNA-directed RNA polymerases II, IV and V subunit 8B Arabidopsis thaliana 0.016626298999999997 1 LEVO MASNIIMFEDIFVVDKLDPDGKKFDKVTRVEARSHNLEMFMHLDVNTEVYPLAVGDKFTLAMAPTLNLDGTPDTGYFTPG AKKTLADKYEYIMHGKLYKISERDGKTPKAELYVSFGGLLMLLQGDPAHISHFELDQRLFLLMRKL Q9M1A8 DNA-directed RNA polymerases II, IV and V subunit 9A Arabidopsis thaliana 0.013297145 1 LEVO MSTMKFCRECNNILYPKEDKEQKILLYACRNCDHQEVADNSCVYRNEVHHSVSERTQILTDVASDPTLPRTKAVRCSKCQ HREAVFFQATARGEEGMTLFFVCCNPNCGHRWRE Q6NLH0 DNA-directed RNA polymerases II, IV and V subunit 10 Arabidopsis thaliana 0.00832369 1 LEVO MIIPVRCFTCGKVIGNKWDQYLDLLQLDYTEGDALDALQLVRYCCRRMLMTHVDLIEKLLNYNTLEKSDNS Q8LFJ6 DNA-directed RNA polymerases II, IV and V subunit 11 Arabidopsis thaliana 0.013582285999999999 1 LEVO MNAPERYERFVVPEGTKKVSYDRDTKIINAASFTVEREDHTIGNIVRMQLHRDENVLFAGYQLPHPLKYKIIVRIHTTSQ SSPMQAYNQAINDLDKELDYLKNQFEAEVAKFSNQF Q38859 DNA-directed RNA polymerases II, IV and V subunit 12 Arabidopsis thaliana 0.005905768 1 LEVO MDPAPEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR Q9FLM8 RNA-dependent RNA polymerase 2 Arabidopsis thaliana 0.129494531 1 LEVO MVSETTTNRSTVKISNVPQTIVADELLRFLELHLGEDTVFALEIPTTRDNWKPRDFARVQFTTLEVKSRAQLLSSQSKLL FKTHNLRLSEAYDDIIPRPVDPRKRLDDIVLTVGFPESDEKRFCALEKWDGVRCWILTEKRRVEFWVWESGDCYKIEVRF EDIIETLSCCVNGDASEIDAFLLKLKYGPKVFKRVTVHIATKFKSDRYRFCKEDFDFMWIRTTDFSGSKSIGTSTCFCLE VHNGSTMLDIFSGLPYYREDTLSLTYVDGKTFASAAQIVPLLNAAILGLEFPYEILFQLNALVHAQKISLFAASDMELIK ILRGMSLETALVILKKLHQQSSICYDPVFFVKTQMQSVVKKMKHSPASAYKRLTEQNIMSCQRAYVTPSKIYLLGPELET ANYVVKNFAEHVSDFMRVTFVEEDWSKLPANALSVNSKEGYFVKPSRTNIYNRVLSILGEGITVGPKRFEFLAFSASQLR GNSVWMFASNEKVKAEDIREWMGCFRKIRSISKCAARMGQLFSASRQTLIVRAQDVEQIPDIEVTTDGADYCFSDGIGKI SLAFAKQVAQKCGLSHVPSAFQIRYGGYKGVIAVDRSSFRKLSLRDSMLKFDSNNRMLNVTRWTESMPCFLNREIICLLS TLGIEDAMFEAMQAVHLSMLGNMLEDRDAALNVLQKLSGENSKNLLVKMLLQGYAPSSEPYLSMMLRVHHESQLSELKSR CRILVPKGRILIGCMDEMGILEYGQVYVRVTLTKAELKSRDQSYFRKIDEETSVVIGKVVVTKNPCLHPGDIRVLDAIYE VHFEEKGYLDCIIFPQKGERPHPNECSGGDLDGDQFFVSWDEKIIPSEMDPPMDYAGSRPRLMDHDVTLEEIHKFFVDYM ISDTLGVISTAHLVHADRDPEKARSQKCLELANLHSRAVDFAKTGAPAEMPYALKPREFPDFLERFEKPTYISESVFGKL YRAVKSSLAQRKPEAESEDTVAYDVTLEEAGFESFIETAKAHRDMYGEKLTSLMIYYGAANEEEILTGILKTKEMYLARD NRRYGDMKDRITLSVKDLHKEAMGWFEKSCEDEQQKKKLASAWYYVTYNPNHRDEKLTFLSFPWIVGDVLLDIKAENAQR QSVEEKTSGLVSI O82504 2.7.7.48 DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*TP*G)-3') synthetic construct 0.006196 1 (DC)(DT)(DG)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC)(DG)(DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG) DNA RNA (39-MER) synthetic construct 0.01221502 1 UUUUAUCGAGAGGUACUUUUCUUUUCUUUCUUCUUCGGU DNA (33-MER) synthetic construct 0.009954427 1 (DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG)(DA)(DT)(DA)(DA)(DG)(DC)(DA)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC)(DC)(DT)(DA)(DT) DNA RNA (5'-R(*CP*CP*GP*A)-3') synthetic construct 0.001239818 1 CCGA ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 2 MG singleParticle particle 1.1 7.5 20.0 C2H18N2O4S HEPES 100.0 NaCl Sodium chloride 5.0 MgCl2 magnesium chloride 2.0 C4H10O2S2 DL-dithiothreitol C-flat-1.2/1.3 COPPER 400 CARBON HOLEY 120.0 GLOW DISCHARGE 120 OTHER ETHANE 95 282.65 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 2.2 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-32 1.95 1 3.16 FSC 0.143 CUT-OFF RELION 3 63253 MAXIMUM LIKELIHOOD RELION 3 MAXIMUM LIKELIHOOD RELION 3 emd_31305_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 296.8 296.8 296.8 90.0 90.0 90.0 X Y Z -0.030017784 0.06922732 0.000038610964 0.0027828985 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-31305:::: emd_31305_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 296.8 296.8 296.8 90.0 90.0 90.0 X Y Z -0.06385517 0.10535088 0.00004751879 0.0064829723 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-31305:::: emd_31305_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 296.8 296.8 296.8 90.0 90.0 90.0 X Y Z -0.065377414 0.10735343 0.00004656031 0.0065332893 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-31305::::