RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome

2026-04-15 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2025-04-17 2026-04-15 2026-04-15 2026-04-15 Japan Society for the Promotion of Science (JSPS) JP20H03201 Japan Japan Society for the Promotion of Science (JSPS) JP20H05690 Japan Japan Society for the Promotion of Science (JSPS) JP22K15033 Japan Japan Society for the Promotion of Science (JSPS) JP23K17392 Japan Japan Society for the Promotion of Science (JSPS) JP22K06098 Japan Japan Society for the Promotion of Science (JSPS) JP23H05475 Japan Japan Society for the Promotion of Science (JSPS) JP24H02328 Japan Japan Science and Technology JPMJER1901 Japan Japan Agency for Medical Research and Development (AMED) JP24ama121009 Japan RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Ho C-H Nozawa K Nishimura M Oi M Kujirai T Ogasawara M Ehara H Sekine S Takizawa Y Kurumizaka H RNAPII, subnucleosome, TRANSCRIPTION, TRANSCRIPTION-RNA-DNA complex Ho CH Nozawa K Nishimura M Oi M Kujirai T Ogasawara M Ehara H Sekine SI Takizawa Y Kurumizaka H Structural basis of RNA polymerase II transcription on the histone H3-H4 octasome. J.Biol.Chem. US 302 111340 111340 2026 41791711 doi:10.1016/j.jbc.2026.111340 1083-351X 0071 JBCHA3 9ujs FULLOVERLAP EMDB EMD-64225 associated EM volume

PDB 9UJT unspecified RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 RNA Polymerase II elongation complex 1 1 2 3 4 5 6 7 8 9 10 11 12 Komagataella phaffii GS115 H3-H4 octasome 1 16 17 Homo sapiens DNA,RNA 1 13 14 15 DNA-directed RNA polymerase subunit Komagataella phaffii GS115 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 GS115 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 GS115 0.034216292999999995 1 LEVO MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMK YSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAK KGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKA NQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY C4R7L2 RNA polymerase II subunit B32 Komagataella phaffii GS115 0.02062298 1 LEVO MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESS NGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLI PSLAAKKEVNLQRILDELNRLEDPYK C4R2U9 RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III Komagataella phaffii GS115 0.024962679999999998 1 LEVO MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVE FCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEK SQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL C4R3P8 RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III Komagataella phaffii GS115 0.017803588 1 LEVO MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERT TTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN C4R1V1 RNA polymerase II subunit Komagataella phaffii GS115 0.018802625 1 LEVO MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWK PFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAI GSIKEDFLGAI C4R9A1 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Komagataella phaffii GS115 0.016249219999999998 1 LEVO MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRP PKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR C4R273 DNA-directed RNA polymerase subunit Komagataella phaffii GS115 0.013612319999999999 1 LEVO MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHS RDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE F2QPE6 RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III Komagataella phaffii GS115 0.008554064 1 LEVO MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS C4R009 RNA polymerase II subunit B12.5 Komagataella phaffii GS115 0.013832896 1 LEVO MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEG TRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND C4R3Z5 RNA polymerase subunit ABC10-alpha Komagataella phaffii GS115 0.007862048 1 LEVO MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR F2QMI1 RNA (5'-R(P*GP*UP*GP*GP*CP*CP*GP*UP*UP*UP*U)-3') synthetic construct 0.003477058 1 GUGGCCGUUUU DNA (198-MER) synthetic construct 0.061372891 1 (DG)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG) (DG)(DG)(DT)(DG)(DG)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DT)(DC)(DG)(DT)(DT)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG)(DT)(DC)(DT)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DT)(DG)(DT)(DC)(DT)(DT)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DT)(DA)(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)(DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT) DNA DNA (198-MER) synthetic construct 0.06087899199999999 1 (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(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)(DT)(DA)(DA)(DA)(DC)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DA)(DC)(DA)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DA)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DC)(DA) (DA)(DC)(DG)(DA)(DA)(DA)(DA)(DC)(DG)(DG)(DC)(DC)(DA)(DC)(DC)(DA)(DC)(DC)(DC)(DA) (DA)(DA)(DC)(DA)(DC)(DA)(DC)(DC)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DA)(DG)(DA)(DG)(DC) (DT)(DA)(DA)(DT)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DG)(DT)(DA)(DA)(DG)(DC) DNA Histone H3.1 Homo sapiens 0.015719445 4 Escherichia coli LEVO GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P68431 Histone H4 Homo sapiens 0.011676702999999998 4 Escherichia coli LEVO GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA KRKTVTAMDVVYALKRQGRTLYGFGG P62805 singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 3 36878 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3D Initial model

3D initial model generated in RELION.

3.62 FSC 0.143 CUT-OFF cryoSPARC 3Dflex

CryoSPARC 3D flex reconstruction

30000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_64225.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.02307761 0.043381646 0.00008842299 0.0010670323 1.06 1.06 1.06 0.007 AUTHOR ::::EMDATABANK.org::::EMD-64225:::: emd_64225_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.040327758 0.06024851 0.00008891797 0.0016995333 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-64225:::: emd_64225_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 381.59998 381.59998 381.59998 90.0 90.0 90.0 X Y Z -0.038019452 0.063217945 0.00008792714 0.0016734344 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-64225::::