8FOJ: DNA polymerase

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the post RNA handoff state. Determined by electron microscopy at 4.8 Å resolution. Released 31 May 2023.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Saccharomyces cerevisiae, synthetic construct
Chains: 6
Atoms: 17,538
Mol. weight: 362.92 kDa
Ligands: SF4
Released: 31 May 2023

Explore 8FOJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FOJ contains 120 α-helices and 93 β-strands across 4 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 1: 48 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	352-362	11	1
β-strand	365-371	7	1
β-strand	381-386	6	1
β-strand	390-397	8	2
α-helix	403-418	16
β-strand	424-431	8	2
β-strand	442-451	10	2
α-helix	460-463	4
β-strand	471-475	5	2
α-helix	481-488	8
β-strand	496-499	4	1
β-strand	511	1	3
β-strand	515-519	5	1
α-helix	522-524	3
β-strand	525-527	3	1
β-strand	538-548	11	4
β-strand	553-564	12	4
α-helix	577-579	3
β-strand	581-586	6	4
β-strand	610-612	3	4
α-helix	616-630	15
β-strand	634-637	4	4
α-helix	640-644	5
α-helix	645-654	10
α-helix	660-663	4
β-strand	666	1	3
α-helix	682-690	9
β-strand	695-698	4	4
α-helix	702-706	5
α-helix	716-724	9
α-helix	729-731	3
α-helix	738-741	4
α-helix	744-768	25
α-helix	770-781	12
α-helix	785-790	6
α-helix	799-806	8
β-strand	810	1	2
α-helix	811-814	4
α-helix	849-851	3
β-strand	854-856	3	5
β-strand	860-864	5	5
α-helix	868-876	9
α-helix	905-926	22
α-helix	930-948	19
α-helix	951-953	3
α-helix	964-987	24
β-strand	991-995	5	5
β-strand	999-1003	5	5
α-helix	1009-1026	18
β-strand	1033-1043	11	5
β-strand	1049-1054	6	5
β-strand	1064-1069	6	5
α-helix	1072-1074	3
α-helix	1080-1092	13
α-helix	1101-1119	19
α-helix	1124-1127	4
β-strand	1129-1132	4	6
α-helix	1147-1158	12
β-strand	1167-1172	6	6
β-strand	1173	1	7
β-strand	1193-1195	3	6
α-helix	1196-1200	5
α-helix	1202-1204	3
α-helix	1207	1
β-strand	1208	1	7
α-helix	1209	1
α-helix	1210-1213	4
α-helix	1214-1219	6
α-helix	1220-1225	6
α-helix	1234-1239	6
β-strand	1284-1286	3	8
β-strand	1293-1295	3	8
β-strand	1305-1307	3	9
β-strand	1312-1314	3	9
α-helix	1319	1
β-strand	1320	1	9
α-helix	1321-1322	2
α-helix	1323-1342	20
β-strand	1346-1348	3	10
β-strand	1356-1357	2	10
β-strand	1366	1	11
α-helix	1374	1
β-strand	1375	1	11
β-strand	1376-1377	2	10
α-helix	1382-1395	14
α-helix	1398-1403	6
α-helix	1406-1408	3
α-helix	1424-1433	10
α-helix	1435-1449	15

Chain A: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	25-33	9
α-helix	40-43	4
β-strand	45-47	3	12
β-strand	60	1	12
α-helix	65-75	11
β-strand	81-86	6	12
β-strand	103-105	3	12
β-strand	108-112	5	13
α-helix	114-120	7
α-helix	131-150	20
β-strand	157-161	5	13
β-strand	167-171	5	13
α-helix	174-177	4
α-helix	181-191	11
α-helix	209-210	2
α-helix	211-224	14
α-helix	225-232	8
α-helix	238-244	7
α-helix	252-260	9
α-helix	271-284	14
α-helix	290-309	20
β-strand	313	1	13
α-helix	316-319	4
β-strand	325-326	2	12
α-helix	327	1
β-strand	331	1	14
β-strand	337	1	15
β-strand	338	1	14
α-helix	340	1
β-strand	341-342	2	13
α-helix	348-350	3
α-helix	352	1
β-strand	353	1	15
α-helix	373-392	20

Chain B: 31 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	44-54	11
α-helix	65-66	2
α-helix	72-94	23
α-helix	99-112	14
α-helix	121-138	18
α-helix	142-162	21
α-helix	165-173	9
β-strand	181-182	2	16
α-helix	183-184	2
α-helix	185-190	6
α-helix	192-206	15
α-helix	212-221	10
β-strand	225-227	3	16
α-helix	229-231	3
α-helix	233-237	5
β-strand	242-244	3	16
β-strand	247-249	3	16
α-helix	255-281	27
α-helix	288-296	9
α-helix	323-325	3
α-helix	327-330	4
α-helix	335-347	13
α-helix	352-365	14
α-helix	369-379	11
α-helix	388-390	3
α-helix	391-395	5
α-helix	396-402	7
α-helix	412-415	4
α-helix	417-422	6
α-helix	424-426	3
α-helix	435-438	4
α-helix	441-450	10
α-helix	455-466	12
α-helix	470-481	12
α-helix	500-510	11

Chain C: 21 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	254-275	22
α-helix	280-282	3
β-strand	283	1	17
β-strand	294-302	9	17
β-strand	316-319	4	17
α-helix	322-325	4
β-strand	330-333	4	17
β-strand	340-342	3	18
β-strand	347-353	7	17
β-strand	359-366	8	17
α-helix	367-374	8
β-strand	375-376	2	19
α-helix	378-388	11
α-helix	392	1
β-strand	393-398	6	20
α-helix	411-419	9
α-helix	420-424	5
β-strand	428-432	5	20
β-strand	437	1	21
α-helix	441-444	4
α-helix	461-473	13
β-strand	481-485	5	20
β-strand	490	1	21
β-strand	498	1	22
β-strand	500	1	23
α-helix	501-503	3
α-helix	505-508	4
β-strand	515-517	3	20
β-strand	520	1	23
β-strand	522-526	5	24
β-strand	529-533	5	24
α-helix	538-541	4
β-strand	545-547	3	18
α-helix	549-553	5
α-helix	556-567	12
β-strand	569	1	25
α-helix	576-577	2
β-strand	578-579	2	26
β-strand	608-609	2	26
β-strand	612	1	22
α-helix	614-620	7
β-strand	621	1	25
α-helix	623-625	3
β-strand	630-632	3	24
β-strand	640-644	5	24
β-strand	647-651	5	24
β-strand	656	1	27
β-strand	662	1	27
β-strand	665-670	6	20
α-helix	671-672	2
β-strand	682-683	2	19
α-helix	684	1
β-strand	689-691	3	19
α-helix	694-697	4
β-strand	698-703	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase	1	protein	1468	Saccharomyces cerevisiae	P13382 (AlphaFold model)
DNA primase	A	protein	409	Saccharomyces cerevisiae	P10363 (AlphaFold model)
DNA primase large subunit	B	protein	528	Saccharomyces cerevisiae	P20457 (AlphaFold model)
DNA polymerase alpha subunit B	C	protein	705	Saccharomyces cerevisiae	P38121 (AlphaFold model)
template DNA	T	DNA	11	synthetic construct
Primer RNA	P	RNA	10	synthetic construct

Sequence of entity 1 (1), FASTA

>8FOJ_1 DNA polymerase (chains 1)
MSSKSEKLEKLRKLQAARNGTSIDDYEGDESDGDRIYDEIDEKEYRARKRQELLHDDFVV
DDDGVGYVDRGVEEDWREVDNSSSDEDTGNLASKDSKRKKNIKREKDHQITDMLRTQHSK
STLLAHAKKSQKKSIPIDNFDDILGEFESGEVEKPNILLPSKLRENLNSSPTSEFKSSIK
RVNGNDESSHDAGISKKVKIDPDSSTDKYLEIESSPLKLQSRKLRYANDVQDLLDDVENS
PVVATKRQNVLQDTLLANPPSAQSLADEEDDEDSDEDIILKRRTMRSVTTTRRVNIDSRS
NPSTSPFVTAPGTPIGIKGLTPSKSLQSNTDVATLAVNVKKEDVVDPETDTFQMFWLDYC
EVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGL
DNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSN
IFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLS
LSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAA
LAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTF
SSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMY
QVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNL
AGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKK
AKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSE
VDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSR
FYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFK
RLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCP
LSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAY
PGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVM
IKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKYFRREGGNNNGED
INNLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQL
FTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGCTGVMRYKY
SDKQLYNQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMET
GRSVVQKYLNDCGRRYVDMTSIFDFMLN

Sequence of entity 2 (A), FASTA

>8FOJ_2 DNA primase (chains A)
MTNSVKTNGPSSSDMEYYYKSLYPFKHIFNWLNHSPKPSRDMINREFAMAFRSGAYKRYN
SFNSVQDFKAQIEKANPDRFEIGAIYNKPPRERDTLLKSELKALEKELVFDIDMDDYDAF
RTCCSGAQVCSKCWKFISLAMKITNTALREDFGYKDFIWVFSGRRGAHCWVSDKRARALT
DVQRRNVLDYVNVIRDRNTDKRLALKRPYHPHLARSLEQLKPFFVSIMLEEQNPWEDDQH
AIQTLLPALYDKQLIDSLKKYWLDNPRRSSKEKWNDIDQIATSLFKGPKQDSHIIKLREC
KEDLVLMTLYPKLDVEVTKQTIHLLKAPFCIHPATGNVCVPIDESFAPEKAPKLIDLQTE
MEKNNDVSLTALQPFINQFQAYVSSLLKNELGSVKREREDDDEPASLDF

Sequence of entity 3 (B), FASTA

>8FOJ_3 DNA primase large subunit (chains B)
MFRQSKRRIASRKNFSSYDDIVKSELDVGNTNAANQIILSSSSSEEEKKLYARLYESKLS
FYDLPPQGEITLEQFEIWAIDRLKILLEIESCLSRNKSIKEIETIIKPQFQKLLPFNTES
LEDRKKDYYSHFILRLCFCRSKELREKFVRAETFLFKIRFNMLTSTDQTKFVQSLDLPLL
QFISNEEKAELSHQLYQTVSASLQFQLNLNEEHQRKQYFQQEKFIKLPFENVIELVGNRL
VFLKDGYAYLPQFQQLNLLSNEFASKLNQELIKTYQYLPRLNEDDRLLPILNHLSSGYTI
ADFNQQKANQFSENVDDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSL
FLKGIGLSADEALKFWSEAFTRNGNMTMEKFNKEYRYSFRHNYGLEGNRINYKPWDCHTI
LSKPRPGRGDYHGCPFRDWSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEM
THNSASADLEIGEQTHIAHPNLYFERSRQLQKKQQKLEKEKLFNNGNH

Sequence of entity 4 (C), FASTA

>8FOJ_4 DNA polymerase alpha subunit B (chains C)
MSGSIDVITHFGPDADKPEIITALENLTKLHALSVEDLYIKWEQFSNQRRQTHTDLTSKN
IDEFKQFLQLQMEKRANQISSSSKVNTSTKKPVIKKSLNSSPLFGLSIPKTPTLKKRKLH
GPFSLSDSKQTYNVGSEAETNEKGNSSLKLEFTPGMAEDAVGDSAPLSHAKSSDAKTPGS
STFQTPTTNTPTTSRQNVPAGEILDSLNPENIEISSGNPNVGLLSTEEPSYNQVKVEPFY
DAKKYKFRTMRQNLQEASDVLDDQIESFTKIIQNHYKLSPNDFADPTIQSQSEIYAVGRI
VPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAFKGKNANGDYF
TVNSILPLPYPNSPVSTSQELQEFQANLEGSSLKVIVTCGPYFANDNFSLELLQEFIDSI
NNEVKPHVLIMFGPFIDITHPLIASGKLPNFPQFKTQPKTLDELFLKLFTPILKTISPHI
QTVLIPSTKDAISNHAAYPQASLIRKALQLPKRNFKCMANPSSFQINEIYFGCSNVDTFK
DLKEVIKGGTTSSRYRLDRVSEHILQQRRYYPIFPGSIRTRIKPKDVSTKKETNDMESKE
EKVYEHISGADLDVSYLGLTEFVGGFSPDIMIIPSELQHFARVVQNVVVINPGRFIRATG
NRGSYAQITVQCPDLEDGKLTLVEGEEPVYLHNVWKRARVDLIAS

Sequence of entity 5 (T), FASTA

>8FOJ_5 template DNA (chains T)
GCTGCCCGCCT

Sequence of entity 6 (P), FASTA

>8FOJ_6 Primer RNA (chains P)
AGGCGAGCAG

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1

Primary citation

Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase. Yuan, Z., Georgescu, R., Li, H. et al. Nat Commun (2023) 14:3697-3697. DOI 10.1038/s41467-023-39441-1 · PubMed

Other PDB entries of the same protein (UniProt P13382 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FVM 2.3 Å, Crystal structure of yeast DNA polymerase alpha
3OIQ 2.4 Å, Crystal structure of yeast telomere protein Cdc13 OB1 and the catalytic subunit of DNA…
3FLO 2.5 Å, Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in…
4B08 2.67 Å, Yeast DNA polymerase alpha, Selenomethionine protein
4C93 2.69 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha.
4FXD 3.0 Å, Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA
4FYD 3.1 Å, Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
8B9A 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork…
8B9B 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA…
8FOK 3.56 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the DNA…
8FOC 3.7 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase in Apo state…
8FOD 3.8 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in Apo state…

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