2024-07-03 REL PDBj PDBj PDBj 2022-09-30 2022-12-07 2022-12-07 2024-07-03 Japan Society for the Promotion of Science (JSPS) JP20H03201 Japan Japan Society for the Promotion of Science (JSPS) JP18H05534 Japan Japan Society for the Promotion of Science (JSPS) JP20H00449 Japan Japan Society for the Promotion of Science (JSPS) JP20H05690 Japan Japan Agency for Medical Research and Development (AMED) JP22ama121009 Japan Japan Science and Technology JPMJER1901 Japan Hirano R Ehara H Tomoya K Takizawa Y Sekine S Kurumizaka H chromatin, nucleosome, TRANSCRIPTION Hirano R Ehara H Kujirai T Uejima T Takizawa Y Sekine SI Kurumizaka H Nat Commun UK 13 7287 7287 2022 36435862 doi:10.1038/s41467-022-35003-z 2041-1723 8h0w FULLOVERLAP RNA polymerase II transcribing a chromatosome (type II) RNA polymerase II transcribing a chromatosome (type II) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 RNA polymerase II 1 1 2 3 4 5 6 7 8 9 10 11 12 Komagataella phaffii DNA, RNA 1 13 14 15 HIstone 1 16 17 18 19 20 Homo sapiens DNA-directed RNA polymerase subunit Komagataella phaffii 0.19410742199999997 1 LEVO MSQFPYSSAPLRSVKEVQFGLLSPEEIRAISVVKIEYPEIMDESRQRPREGGLNDPKLGSIDRNFKCQTCGEGMAECPGH FGHMELAKPVFHIGFIPKIKKVCECICMNCGKLLLDETNPTMAQAIRIRDPKKRFNAVWQLCKTKMVCEADAPVDEYSEQ KVVSRGGCGNTQPVVRKDGMKLWGTWKKSGFSDRDAQPERKLLTPGEILNVFKHISPEDCFRLGFNEDYARPEWMIITVL PVPPPQVRPSIAMDETTQGQDDLTHKLSDILKANINVQKLEMDGSPQHIINEVEQLLQFHVATYMDNDIAGQPQALQKSG RPVKAIRARLKGKEGRLRGNLMGKRVDFSARTVISGDPNLELDQVGVPISIAKTLSYPETVTQYNIHRLTEYVRNGPNEH PGAKYVIRDNGDRIDLRYHKRAGDIVLQYGWKVERHLMDDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYN ADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEYEQVMNMLFWVPSWDGV VPQPAILKPKPLWTGKQLLSIAIPSGIHLQRTDGGNSLLSPKDNGMLIVDGKVMFGVVDKKTVGSGGGGLIHTVMREKGP KICAELFGNIQKVVNYWLLHNGFSIGIGDAIADASTMKEITHAISSAKEQVQEIIYKAQHNELELKPGMTLRESFEGEVS RTLNDARDSAGRSAEMNLKDLNNVKQMVSAGSKGSFINIAQMSACVGQQMVEGKRIAFGFADRSLPHFTKDDFSPESKGF VENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDGTTRNSLGDIIQFLYGEDGLDGTQVE RQTIDTIPGSDKAFHKRYYVDLMDEKNSIKPDVIEYAADILGDVELQKELNSEYEQLVSDRKFLREIVFVNGDHNWPLPV NLRRIIQNAQQIFHLDRAKASDLTIPEIIHGVRDLCKKLFVLRGENELIKEAQQNATSLFQCLVRARLATRRILEEFRLN RDAFEWVLGTIEAQFQRSLVHPGEMVGVIAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPALTV YLDREIALDIEKAKVIQSSIEYTTLKNVTSATEIYYDPDPTSTVIEEDFDTVEAYFSIPDEKVEETIDKQSPWLLRLELD RARMLDKQLTMNQVADKISEVFSDDLFVMWSEDNADKLIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRGIP GISKVYMVKHKVSVPDESGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEILSVLGIEATRSSLYKEILNVIA FDGSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILFEAGAAAELDDCRGVSENVMLGQLAPMG TGAFDVMIDEKLLTSLPADYAPTMPLFKGKATQGSATPYDNNAQYDDEFNHDDVADVMFSPMAETGSGDDRSGGLTEYAG IQSPYQPTSPGLSATSPGFAPTSPGFAPTSPRYSPTSPGYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP SYSPTSPSYSPTSPSYSPTSPSYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYS PTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPASPQYSPSRHSPNGESKEGE C4R4Y0 2.7.7.6 DNA-directed RNA polymerase subunit beta Komagataella phaffii 0.13974609400000002 1 LEVO MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFG KIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGK VPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSR LISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKE VALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLD LAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYT YSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLE DYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKD NKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLN DTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ KPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRA TTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEG LKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGY EGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVE GRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAA KLLFQELMAMNIAPRLYTERSGVSMRS C4QZQ7 2.7.7.6 RNA polymerase II third largest subunit B44, part of central core Komagataella phaffii 0.034216292999999995 1 LEVO MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMK YSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAK KGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKA NQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY C4R7L2 RNA polymerase II subunit B32 Komagataella phaffii 0.02062298 1 LEVO MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESS NGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLI PSLAAKKEVNLQRILDELNRLEDPYK C4R2U9 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Komagataella phaffii 0.024962679999999998 1 LEVO MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVE FCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEK SQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL C4R3P8 RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III Komagataella phaffii 0.017803588 1 LEVO MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERT TTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN C4R1V1 RNA polymerase II subunit Komagataella phaffii 0.018802625 1 LEVO MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWK PFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAI GSIKEDFLGAI C4R9A1 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Komagataella phaffii 0.016249219999999998 1 LEVO MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRP PKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR C4R273 DNA-directed RNA polymerase subunit Komagataella phaffii 0.013612319999999999 1 LEVO MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHS RDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE F2QPE6 RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III Komagataella phaffii 0.008554064 1 LEVO MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS C4R009 RNA polymerase II subunit B12.5 Komagataella phaffii 0.013832896 1 LEVO MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEG TRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND C4R3Z5 RNA polymerase subunit ABC10-alpha Komagataella phaffii 0.007862048 1 LEVO MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR F2QMI1 RNA (5'-R(P*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*UP*AP*C)-3') synthetic construct 0.0044707309999999995 1 CAAUAGGAGCUUAC DNA (261-MER) synthetic construct 0.08085155499999999 1 (DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DA)(DT)(DT)(DC)(DC)(DC)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DC)(DC)(DA)(DA)(DA)(DC) (DA)(DC)(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DC)(DC)(DG)(DT)(DA)(DA)(DG)(DC)(DT)(DC)(DC) (DT)(DA)(DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA)(DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG) (DA)(DC)(DA)(DA)(DA)(DC)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DA)(DA)(DT)(DG)(DA)(DG) (DA)(DG)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DT)(DA)(DA)(DG)(DA) (DA) DNA DNA (261-MER) synthetic construct 0.08032907799999998 1 (DT)(DT)(DC)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DT)(DT)(DA)(DG)(DC) (DT)(DC)(DT)(DC)(DA)(DT)(DT)(DC)(DC)(DG)(DG)(DA)(DC)(DG)(DT)(DG)(DT)(DT)(DT)(DG) (DT)(DC)(DC)(DT)(DC)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DA)(DA)(DG)(DC)(DA)(DA)(DT) (DA)(DG)(DG)(DA)(DG)(DC)(DT)(DT)(DA)(DC)(DG)(DG)(DT)(DC)(DC)(DA)(DC)(DT)(DT)(DG) (DT)(DG)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DG)(DA)(DA)(DT) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DC)(DT) (DT)(DG)(DT)(DG)(DT)(DC)(DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DA)(DT)(DA)(DG)(DA) (DT) DNA Histone H3.1 Homo sapiens 0.015719445 2 Escherichia coli LEVO GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P68431 Histone H4 Homo sapiens 0.011676702999999998 2 Escherichia coli LEVO GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA KRKTVTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1-B/E Homo sapiens 0.014447825 2 Escherichia coli LEVO GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKT RIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P04908 Histone H2B type 1-J Homo sapiens 0.014217516 2 Escherichia coli LEVO GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGE ASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P06899 Histone H1.2 Homo sapiens 0.02215684 1 Escherichia coli LEVO MSETAPAAPAAAPPAEKAPVKKKAAKKAGGTPRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRI KLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKVKKAGGTKPKKPVGAAKKPKKAAGGATPKKSAKKTPKKAKK PAAATVTKKVAKSPKKAKVAKPKKAAKSAAKAVKPKAAKPKVVKPKKAAPKKKLEVLFQ P16403 ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 2.3000000000000003 GATAN K3 BIOQUANTUM (6k x 4k) 56.2 1 4.6 FSC 0.143 CUT-OFF 16916 MAXIMUM LIKELIHOOD emd_34416_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 357.6 357.6 357.6 90.0 90.0 90.0 X Y Z -0.015128876 0.07717286 0.00013907773 0.003341071 1.49 1.49 1.49 AUTHOR ::::EMDATABANK.org::::EMD-34416:::: Nucleosome reconstruction emd_34416_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 357.6 357.6 357.6 90.0 90.0 90.0 X Y Z -0.05004389 0.12536627 0.00022975387 0.004156516 1.49 1.49 1.49 AUTHOR ::::EMDATABANK.org::::EMD-34416:::: RNAP reconstruction emd_34416_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 357.6 357.6 357.6 90.0 90.0 90.0 X Y Z -0.07763188 0.12868619 0.00031577813 0.008511062 1.49 1.49 1.49 AUTHOR ::::EMDATABANK.org::::EMD-34416:::: emd_34416_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 357.6 357.6 357.6 90.0 90.0 90.0 X Y Z -0.077447034 0.14299412 0.00027163565 0.008415284 1.49 1.49 1.49 AUTHOR ::::EMDATABANK.org::::EMD-34416::::