9G23: DNA-directed RNA polymerase I subunit RPA190

Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site. Determined by electron microscopy at 3.4 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 17
Atoms: 34,137
Mol. weight: 618.17 kDa
Ligands: ZN, MG, APC
Released: 18 Jun 2025

Explore 9G23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9G23 contains 189 α-helices and 247 β-strands across 14 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 74 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	11-18	8	1
α-helix	21-27	7
β-strand	31	1	2
β-strand	38	1	3
β-strand	44	1	3
α-helix	52-54	3
α-helix	61-62	2
β-strand	77-86	10	2
α-helix	91-98	8
β-strand	101	1	4
β-strand	108	1	4
α-helix	112-127	16
α-helix	132-135	4
α-helix	177-198	22
α-helix	210-229	20
β-strand	233	1	5
β-strand	238	1	5
α-helix	241	1
β-strand	242-246	5	6
β-strand	250-254	5	6
α-helix	260-267	8
β-strand	313-314	2	6
α-helix	317-330	14
α-helix	332-338	7
α-helix	348-350	3
β-strand	356-362	7	2
α-helix	363-364	2
α-helix	369-370	2
β-strand	371-372	2	7
β-strand	377-378	2	7
α-helix	381-408	28
α-helix	413-438	26
α-helix	452-454	3
α-helix	457-459	3
α-helix	466-470	5
β-strand	475-476	2	8
β-strand	479-486	8	9
β-strand	494-497	4	9
α-helix	499-502	4
β-strand	506-510	5	10
α-helix	511	1
α-helix	516-525	10
β-strand	533-537	5	10
β-strand	543-545	3	10
α-helix	551-559	9
β-strand	576-580	5	10
β-strand	586-590	5	9
α-helix	597-599	3
β-strand	600-607	8	9
β-strand	614-616	3	9
α-helix	620-624	5
β-strand	632-636	5	9
α-helix	641-647	7
β-strand	652	1	9
α-helix	653-656	4
β-strand	658	1	11
β-strand	665	1	11
α-helix	672-681	10
β-strand	686-687	2	12
α-helix	689-697	9
β-strand	719-721	3	13
β-strand	725	1	13
β-strand	726-727	2	12
α-helix	728-739	12
β-strand	750-752	3	14
β-strand	768-772	5	14
β-strand	775-778	4	14
α-helix	793-823	31
β-strand	826-827	2	15
α-helix	831-833	3
β-strand	835	1	16
α-helix	837-847	11
α-helix	848-850	3
α-helix	853-861	9
α-helix	864-865	2
α-helix	873-884	12
α-helix	887-911	25
β-strand	916	1	16
α-helix	924-930	7
α-helix	937-944	8
β-strand	949	1	17
α-helix	977-979	3
β-strand	981	1	17
β-strand	985	1	18
β-strand	989	1	18
α-helix	992-1027	36
β-strand	1031-1032	2	19
β-strand	1038-1039	2	19
β-strand	1045	1	19
β-strand	1055	1	20
α-helix	1066-1071	6
α-helix	1073-1080	8
α-helix	1082-1084	3
β-strand	1090	1	21
α-helix	1092-1107	16
α-helix	1123-1126	4
β-strand	1132	1	21
α-helix	1138-1150	13
α-helix	1163-1176	14
β-strand	1178	1	20
α-helix	1179-1180	2
α-helix	1185-1194	10
α-helix	1195-1199	5
α-helix	1219-1225	7
β-strand	1238-1241	4	22
β-strand	1242	1	23
α-helix	1243	1
α-helix	1252-1258	7
β-strand	1261-1262	2	24
β-strand	1267-1275	9	25
β-strand	1288	1	26
β-strand	1289-1296	8	25
α-helix	1299-1305	7
α-helix	1310-1316	7
α-helix	1317-1321	5
α-helix	1322-1337	16
α-helix	1435-1437	3
α-helix	1441-1453	13
β-strand	1471-1473	3	25
β-strand	1476	1	26
α-helix	1487-1495	9
β-strand	1497-1499	3	24
β-strand	1507-1508	2	22
α-helix	1510-1512	3
β-strand	1518-1521	4	22
α-helix	1526-1531	6
β-strand	1536	1	23
α-helix	1538-1540	3
β-strand	1542-1543	2	22
α-helix	1547-1553	7
α-helix	1555-1572	18
α-helix	1579-1589	11
α-helix	1600-1602	3
α-helix	1609-1615	7
α-helix	1618-1626	9
β-strand	1631-1632	2	1
α-helix	1637-1643	7
α-helix	1650-1652	3
β-strand	1654-1660	7	27

Chain B: 54 helices, 81 β-strands

Element	Residues	Length	Sheet
α-helix	18-26	9
α-helix	36-41	6
α-helix	43-51	9
α-helix	56-58	3
α-helix	60-68	9
β-strand	71-74	4	28
β-strand	94-97	4	28
β-strand	99-104	6	28
β-strand	108-109	2	29
α-helix	118	1
β-strand	119-120	2	29
α-helix	123-129	7
β-strand	134-145	12	28
β-strand	150-162	13	28
β-strand	164	1	30
α-helix	177-182	6
β-strand	194-196	3	30
β-strand	199-201	3	30
β-strand	202-203	2	31
β-strand	205-209	5	32
α-helix	210	1
β-strand	211	1	33
β-strand	215-216	2	33
α-helix	220-223	4
β-strand	233-240	8	33
β-strand	244-251	8	33
β-strand	253	1	34
β-strand	257	1	34
β-strand	259-262	4	33
β-strand	269-272	4	33
α-helix	273-280	8
α-helix	285-292	8
α-helix	300-316	17
α-helix	323-333	11
α-helix	346-357	12
α-helix	360-362	3
α-helix	367-385	19
α-helix	390-393	4
α-helix	397-399	3
β-strand	400-403	4	32
α-helix	406-433	28
α-helix	443-450	8
α-helix	457-467	11
β-strand	485-486	2	31
α-helix	493-499	7
β-strand	502	1	35
β-strand	503-504	2	32
α-helix	507-510	4
α-helix	515-517	3
α-helix	522-524	3
β-strand	528	1	36
β-strand	544	1	35
β-strand	545	1	36
β-strand	550-551	2	37
α-helix	552	1
α-helix	561-567	7
α-helix	570	1
β-strand	571-572	2	38
β-strand	584-588	5	38
β-strand	591-596	6	38
α-helix	598-613	16
β-strand	625-629	5	38
β-strand	639-643	5	38
β-strand	649-650	2	37
β-strand	651-655	5	39
α-helix	657-659	3
β-strand	661-664	4	39
α-helix	666-669	4
β-strand	674-675	2	39
α-helix	678-680	3
β-strand	688-689	2	39
α-helix	693-696	4
α-helix	707-709	3
β-strand	710	1	40
α-helix	712-721	10
β-strand	725	1	41
α-helix	733-735	3
β-strand	740-744	5	42
β-strand	748	1	43
β-strand	752-753	2	44
α-helix	756-759	4
α-helix	762-764	3
β-strand	769-775	7	45
β-strand	776-777	2	15
β-strand	787-790	4	45
α-helix	791-794	4
β-strand	801-810	10	42
β-strand	823-825	3	46
α-helix	834-838	5
β-strand	840	1	47
β-strand	846	1	47
α-helix	847	1
β-strand	851-852	2	42
β-strand	857-863	7	46
β-strand	868-873	6	46
β-strand	880-888	9	42
β-strand	900-908	9	42
β-strand	916	1	48
β-strand	917-919	3	45
β-strand	926	1	48
β-strand	927-931	5	45
β-strand	939	1	49
β-strand	947-949	3	45
α-helix	953-957	5
β-strand	959	1	40
α-helix	960-975	16
β-strand	979-980	2	44
α-helix	992-1003	12
β-strand	1010-1011	2	45
β-strand	1013	1	49
β-strand	1014	1	50
β-strand	1021	1	50
α-helix	1022	1
β-strand	1026-1035	10	45
β-strand	1036	1	41
α-helix	1040-1042	3
β-strand	1045-1047	3	9
β-strand	1052	1	51
α-helix	1058	1
β-strand	1059	1	51
α-helix	1060	1
α-helix	1067-1068	2
β-strand	1069-1070	2	8
α-helix	1073-1081	9
α-helix	1085-1089	5
α-helix	1090-1094	5
β-strand	1098-1104	7	52
β-strand	1113-1115	3	53
β-strand	1126-1128	3	53
β-strand	1133-1134	2	54
β-strand	1158-1160	3	54
β-strand	1166-1168	3	54
β-strand	1173-1179	7	52
α-helix	1180-1191	12
β-strand	1194-1200	7	1

Chain C: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	33-39	7
β-strand	41-42	2	55
β-strand	51-57	7	55
α-helix	61-73	13
β-strand	77-88	12	56
α-helix	94-102	9
β-strand	106	1	57
α-helix	110-112	3
α-helix	115-117	3
α-helix	122-125	4
β-strand	132-139	8	56
β-strand	141-142	2	58
α-helix	146-147	2
α-helix	153-156	4
β-strand	157-158	2	58
β-strand	161-163	3	59
α-helix	164-166	3
β-strand	168-170	3	56
α-helix	175-178	4
β-strand	186	1	57
β-strand	192-195	4	59
β-strand	201-211	11	56
α-helix	217-219	3
β-strand	222-226	5	55
β-strand	229-235	7	55
α-helix	242-249	8
β-strand	256-259	4	60
β-strand	264-267	4	60
α-helix	279-281	3
β-strand	289-304	16	55
α-helix	310-330	21
α-helix	332-333	2
β-strand	334	1	61

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	27
β-strand	29-30	2	27
α-helix	37-43	7

Chain E: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
β-strand	28	1	62
α-helix	39-45	7
β-strand	60-62	3	63
β-strand	64	1	62
α-helix	66-71	6
β-strand	78-82	5	63
α-helix	90-102	13
β-strand	107-112	6	63
α-helix	118-123	6
α-helix	124-126	3
β-strand	131-136	6	63
α-helix	144-146	3
β-strand	152-155	4	64
α-helix	158-168	11
α-helix	172-174	3
α-helix	176	1
β-strand	177-178	2	64
α-helix	183-188	6
α-helix	190-191	2
α-helix	194	1
β-strand	195-202	8	64
β-strand	206-214	9	64

Chain F: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	56-72	17
β-strand	73	1	27
α-helix	74-75	2
α-helix	76-78	3
β-strand	84	1	65
α-helix	85-86	2
α-helix	87-102	16
α-helix	117-127	11
β-strand	132-137	6	27
β-strand	143-147	5	27
β-strand	152	1	65

Chain G: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	38-49	12	27
α-helix	57-61	5
α-helix	62-66	5
α-helix	67-69	3
β-strand	70	1	27
β-strand	73	1	66
β-strand	80	1	66
β-strand	81-89	9	27
β-strand	103-107	5	27
α-helix	108	1
β-strand	114-125	12	27
β-strand	132-135	4	67
β-strand	136-140	5	68
β-strand	145-148	4	68
β-strand	149	1	69
β-strand	153	1	69
α-helix	223-225	3
β-strand	229-232	4	67
β-strand	235-237	3	70
β-strand	244-246	3	70

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	13
β-strand	14-16	3	71
β-strand	23-29	7	71
β-strand	30	1	13
β-strand	37-43	7	71
β-strand	54-60	7	13
α-helix	89-91	3
β-strand	95-97	3	13
β-strand	100-106	7	71
β-strand	112-118	7	71
β-strand	121-126	6	71
α-helix	129-132	4
β-strand	139	1	71
β-strand	141-145	5	13

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase I subunit RPA190	A	protein	1664	Saccharomyces cerevisiae	P10964 (AlphaFold model)
DNA-directed RNA polymerase I subunit RPA135	B	protein	1203	Saccharomyces cerevisiae	P22138 (AlphaFold model)
DNA-directed RNA polymerases I and III subunit RPAC1	C	protein	335	Saccharomyces cerevisiae	P07703 (AlphaFold model)
DNA-directed RNA polymerase I subunit RPA14	D	protein	137	Saccharomyces cerevisiae	P50106 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae	P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae	P20435
DNA-directed RNA polymerase I subunit RPA43	G	protein	326	Saccharomyces cerevisiae	P46669
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	146	Saccharomyces cerevisiae	P20436
DNA-directed RNA polymerase I subunit RPA12	I	protein	125	Saccharomyces cerevisiae	P32529
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	70	Saccharomyces cerevisiae	P22139
DNA-directed RNA polymerases I and III subunit RPAC2	K	protein	142	Saccharomyces cerevisiae	P28000
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	70	Saccharomyces cerevisiae	P40422

5 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9G23_1 DNA-directed RNA polymerase I subunit RPA190 (chains A)
MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLYDLALGAFLRN
LCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRASCLFCHHFRLKSVEVHRYAC
KLRLLQYGLIDESYKLDEITLGSLNSSMYTDDEAIEDNEDEMDGEGSKQSKDISSTLLNE
LKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGKCDNCGMFS
PKFRKDGFTKIFETALNEKQITNNRVKGFIRQDMIKKQKQAKKLDGSNEASANDEESFDV
GRNPTTRPKTGSTYILSTEVKNILDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVL
VVPPTRFRLPSKLGEEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIF
SRLMNAFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKHMMGKRVNYAA
RSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQIQNED
GSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNKKVYRHIKNRDVVLMNRQPTLHKASM
MGHKVRVLPNEKTLRLHYANTGAYNADFDGDEMNMHFPQNENARAEALNLANTDSQYLTP
TSGSPVRGLIQDHISAGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIF
KPYPLWTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLCGI
LDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATAFTCGMDDLRLTAEGN
KWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKRLQEILRDNNKSGILDAVTSSKV
NAITSQVVSKCVPDGTMKKFPCNSMQAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVM
VSGKTLPSFKPYETDAMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQ
RCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLKKY
NPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLAKYNPAKYLGSVSENF
QDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQM
TLNTFHFAGHGAANVTLGIPRLREIVMTASAAIKTPQMTLPIWNDVSDEQADTFCKSISK
VLLSEVIDKVIVTETTGTSNTAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVISNQ
FIHLLEAAIVKEIKKQKRTTGPDIGVAVPRLQTDVANSSSNSKRLEEDNDEEQSHKKTKQ
AVSYDEPDEDEIETMREAEKSSDEEGIDSDKESDSDSEDEDVDMNEQINKSIVEANNNMN
KVQRDRQSAIISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQ
IPHIDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARN
TIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQGMETSTSSFMKMSYETTCQ
FLTKAVLDNEREQLDSPSARIVVGKLNNVGTGSFDVLAKVPNAA

Sequence of entity 2 (B), FASTA

>9G23_2 DNA-directed RNA polymerase I subunit RPA135 (chains B)
MSKVIKPPGQARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGL
LNLGVKDIGEKVIFDGKPLNSEDEISNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAVERK
VYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYEL
VQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGASYSHYGIQIRSVR
PDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIFDGIIGNDVKDS
FLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLV
HLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEY
LQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLDLQQ
VSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCG
LLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQ
GKIIADTLRYWKVEGKTPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDK
EDIVGPFEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQ
MGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTG
YDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKL
DEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQT
VSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTI
GMFVESLAGKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATGE
ELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALI
GHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRIGSISTVCCRRCSMRFEDAKK
LLTKSEDGEKIFIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDSELSAMGIRLRYNV
EPK

Sequence of entity 3 (C), FASTA

>9G23_3 DNA-directed RNA polymerases I and III subunit RPAC1 (chains C)
MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINID
TSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNL
PDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQSTTFA
DCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK
GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIF
NVESAGAMTPEEIFFKSVRILKNKAEYLKNCPITQ

Sequence of entity 4 (D), FASTA

>9G23_4 DNA-directed RNA polymerase I subunit RPA14 (chains D)
MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDSTTMNTIS
GNAADADAAAVANTSLNIDTNLSSSISQLKRIQRDFKGLPPAQDFSAAPIQVSTTEKKET
SIGVSATGGKKTTFADE

Sequence of entity 5 (E), FASTA

>9G23_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>9G23_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>9G23_7 DNA-directed RNA polymerase I subunit RPA43 (chains G)
MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQG
VMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHV
NLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDVEEDADVI
NTDENNGNNNNEDNKDSNGGSNSLGKFSFGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG
RVVSVDGTLISDADEEGNGYNSSRSQAESLPIVSNKKIVFDDEVSIENKESHKELDLPEV
KEDNGSEIVYEENTSESNDGESSDSD

Sequence of entity 8 (H), FASTA

>9G23_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>9G23_9 DNA-directed RNA polymerase I subunit RPA12 (chains I)
MSVVGSLIFCLDCGDLLENPNAVLGSNVECSQCKAIYPKSQFSNLKVVTTTADDAFPSSL
RAKKSVVKTSLKKNELKDGATIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGYK
FRTNN

Sequence of entity 10 (J), FASTA

>9G23_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>9G23_11 DNA-directed RNA polymerases I and III subunit RPAC2 (chains K)
MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTS
ASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKG
LKDLMDLCDVVESKFTEKIKSM

Sequence of entity 12 (L), FASTA

>9G23_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	1
APC	Diphosphomethylphosphonic acid adenosyl ester	C11 H18 N5 O12 P3	1

Primary citation

Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions. Santos-Aledo, A., Plaza-Pegueroles, A., Sanz-Murillo, M. et al. Nat Commun (2025) 16:5254-5254. DOI 10.1038/s41467-025-60536-4 · PubMed

Other PDB entries of the same protein (UniProt P10964 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RUI 2.7 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 2
9G1V 2.7 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site
4C2M 2.8 Å, Structure of RNA polymerase I at 2.8 A resolution
9G27 2.8 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation…
6RQL 2.9 Å, RNA Polymerase I Closed Conformation 2 (CC2)
4C3I 3.0 Å, Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100
6RWE 3.0 Å, RNA Polymerase I Open Complex conformation 2
6RRD 3.1 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 1
6HLQ 3.18 Å, Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP
6HLR 3.18 Å, Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused)
9G2B 3.2 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit
6HLS 3.21 Å, Yeast apo RNA polymerase I*

Browse structure collections

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