2023-11-01 REL PDBe PDBe PDBe 2023-08-10 2023-08-30 2023-08-30 2023-11-01 KU Leuven Belgium Goovaerts Q Shen J Patel SS Das K gene transcription, polymerase, RDRP, MTF1, RPO41, mtRNAP, DNA, transcription initiation, RNA polymerase, mitochondria, IC8', IC8, TRANSCRIPTION Goovaerts Q Shen J De Wijngaert B Basu U Patel SS Das K Nature UK 622 872 879 2023 37821701 doi:10.1038/s41586-023-06643-y 1476-4687 0006 NATUAS EMD-10845 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase pre-transcription initiation complex

EMD-10846 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex

EMD-15662 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 4-mer RNA, pppGpGpUpA (IC4)

EMD-15556 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with two GTP molecules poised for de novo initiation (IC2)

EMD-15664 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 5-mer RNA, pppGpGpApApA (IC5)

EMD-15665 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 6-mer RNA, pppGpGpApApApU (IC6)

EMD-16443 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppGpGpUpApApApUpG (IC8)

EMD-16442 other EM volume

Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 7-mer RNA, pppGpGpUpApApApU (IC7)

8q63 FULLOVERLAP alternate state of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppGpGpUpApApApUpG, and a wider polymerase cleft (IC8') alternate state of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppGpGpUpApApApUpG, and a wider polymerase cleft (IC8') 0 1 2 3 4 Saccharomyces cerevisiae S288C 0.204 DNA-directed RNA polymerase, mitochondrial 1 2 Saccharomyces cerevisiae S288C Mitochondrial transcription factor 1 1 1 Saccharomyces cerevisiae S288C DNA (37-mer) 1 3 4

15S mitochondria

Saccharomyces cerevisiae S288C RNA (pppGpGpUpApApApUpG) 1 5 Saccharomyces cerevisiae S288C Mitochondrial transcription factor 1 Saccharomyces cerevisiae S288C ATCC 204508 / S288C 0.041151203 1 Escherichia coli BL21(DE3) LEVO MGGSHHHHHHGMASSVPIPGIKDISKLKFFYGFKYLWNPTVYNKIFDKLDLTKTYKHPEELKVLDLYPGVGIQSAIFYNK YCPRQYSLLEKRSSLYKFLNAKFEGSPLQILKRDPYDWSTYSNLIDEERIFVPEVQSSDHINDKFLTVANVTGEGSEGLI MQWLSCIGNKNWLYRFGKVKMLLWMPSTTARKLLARPGMHSRSKCSVVREAFTDTKLIAISDANELKGFDSQCIEEWDPI LFSAAEIWPTKGKPIALVEMDPIDFDFDVDNWDYVTRHLMILKRTPLNTVMDSLGHGGQQYFNSRITDKDLLKKCPIDLT NDEFIYLTKLFMEWPFKPDILMDFVDMYQTEHSG P14908 2.1.1.- DNA-directed RNA polymerase, mitochondrial Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.14328265599999998 1 Escherichia coli BL21(DE3) LEVO GAMGSGIQRPSAVTSMTRTRDVMQLWSLLEACLQSNLMKRAFSILESLYLVPEHKQRFIEDYNMYLNSFSKNDPNFPILK MNEKLTNDLETSFKDVNYNDKTLAIMIHHALNFHSTTSSMLLKPIISAYLKMSVNGIREIFSCLDILTISDLNILMNDLK VITPSQLPNSVRPILESLTLSPTPVNNIENEEGLNKVEAENDSKLHKASNASSDSIKKPSLDPLREVSFHGSTEVLSKDA EKLIAVDTIGMRVIRHTLLGLSLTPEQKEQISKFKFDANDNVLKMKPTKNDDNNNSINFFEIYNSLPTLEEKKAFESALN IFNQDRQKVLENRATEAARERWKHDFEEAKARGDISIEKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKGLNKV DTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGGVIEGMRTARAVISVGKAIEMEFRSEQVLKSESQAFRDVNKKSPEF KKLVQNAKSVFRSSQIEQSKILWPQSIRARIGSVLISMLIQVAKVSVQGVDPVTKAKVHGEAPAFAHGYQYHNGSKLGVL KIHKTLIRQLNGERLIASVQPQLLPMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASDNGDIDRVYDGLNVL GRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMVLPPAPPKNSDPSILRAWKLQVKTIANKFSSDRSNRCDTNYKLEI ARAFLGEKLYFPHNLDFRGRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWLKIHLSNLFGFDKLPLKDRVAFTES HLQDIKDSAENPLTGDRWWTTADKPWQALATCFELNEVMKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGATQVNL VPSDKPQDVYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQTVMTNVYGVTYVGATFQIAKQLSPIFDDRKESLD FSKYLTKHVFSAIRELFHSAHLIQDWLGESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLGLPIVQPYREESKKQ VETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSLDASHMLLSAAECGKQGLDFASVHDSYWTHASDIDTMNVVLREQF IKLHEVDLVLRLKEEFDQRYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTLADEIYFEKKRQELLNSPLIEDRNV GEKMVTTVSLFEDITDLDALELENGGDENSGMSVLLPLRLPEIPPKGDFDVTVLRNSQYFFS P13433 2.7.7.6 Non-template DNA (37-mer) Saccharomyces cerevisiae S288C 0.011468459 1 (DC)(DG)(DA)(DA)(DT)(DA)(DA)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT)(DA)(DT)(DA)(DA)(DG) (DT)(DA)(DA)(DT)(DA)(DA)(DA)(DT)(DG)(DC)(DA)(DA)(DA)(DT)(DT)(DG)(DC) DNA Template DNA (37-MER) Saccharomyces cerevisiae S288C 0.011298308 1 (DG)(DC)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DA)(DT)(DT)(DT)(DA)(DC)(DC)(DG)(DA)(DC)(DA) (DA)(DT)(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DT)(DT)(DA)(DT)(DT)(DC)(DG) DNA RNA (pppGpGpUpApApApUpG) Saccharomyces cerevisiae S288C 0.0022454029999999995 1 GUAAAUG GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 1 GTP singleParticle particle 0.5 7.0

50 mM Bis-Tris propane; 100 mM NaCl, 5 mM MgCl2, 1 mM EDTA, 2 mM DTT

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 45 AIR 0.03 ETHANE 95 281.15 LEICA EM GP

3 ul sample, back blotting for 12 seconds.

TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 0.55 1.8 2.6 150000.0 OTHER NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 1409 37.06 40.0 1 877163 6YMV C1 3.68 FSC 0.143 CUT-OFF RELION 129204 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 FLEXIBLE FIT

Realspace refinement

Correlation coefficient REAL 80.0 emd_18183_msk_1.map emd_18183_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 126.100006 126.100006 126.100006 90.0 90.0 90.0 X Y Z -0.047923077 0.08501888 0.0005423709 0.007922957 0.97 0.97 0.97 AUTHOR ::::EMDATABANK.org::::EMD-18183:::: emd_18183_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 130 130 0 0 0 130 130 130 126.100006 126.100006 126.100006 90.0 90.0 90.0 X Y Z -0.04254431 0.088270366 0.0005375318 0.007933231 0.97 0.97 0.97 AUTHOR ::::EMDATABANK.org::::EMD-18183::::