4FXD: Yeast DNA polymerase alpha

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA. Determined by X-ray diffraction at 3.0 Å resolution. Released 27 Feb 2013.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 13,910
Mol. weight: 223.24 kDa
Released: 27 Feb 2013

Explore 4FXD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FXD contains 79 α-helices and 66 β-strands across 2 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: 40 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	352-362	11	1
β-strand	365-373	9	1
β-strand	379-386	8	1
β-strand	390-397	8	2
α-helix	403-418	16
β-strand	425-431	7	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	503	1	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	536-548	13	4
β-strand	553-567	15	4
α-helix	572-574	3
α-helix	577-579	3
β-strand	581-586	6	4
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-612	4	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	680-691	12
β-strand	695-698	4	4
α-helix	702-706	5
α-helix	716-724	9
α-helix	739-742	4
α-helix	744-767	24
α-helix	770-781	12
α-helix	785-790	6
α-helix	796-807	12
β-strand	810	1	2
α-helix	811-814	4
β-strand	849	1	5
β-strand	854-856	3	5
β-strand	860-864	5	5
α-helix	868-875	8
α-helix	896-898	3
α-helix	902-903	2
α-helix	905-926	22
α-helix	930-947	18
α-helix	951-955	5
α-helix	964-987	24
β-strand	991-995	5	5
β-strand	999-1003	5	5
α-helix	1009-1026	18
β-strand	1033-1045	13	5
β-strand	1048-1056	9	5
β-strand	1062-1069	8	5
α-helix	1072-1074	3
α-helix	1080-1093	14
α-helix	1099-1118	20
α-helix	1124-1127	4
β-strand	1129-1133	5	6
α-helix	1147-1158	12
β-strand	1166-1172	7	6
β-strand	1173	1	7
β-strand	1193-1195	3	6
α-helix	1196-1200	5
α-helix	1202-1204	3
β-strand	1208	1	7
α-helix	1210-1212	3
α-helix	1213-1219	7
α-helix	1220-1225	6
α-helix	1234-1239	6

Chain B: 39 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	352-362	11	8
β-strand	365-373	9	8
β-strand	379-386	8	8
β-strand	390-397	8	9
α-helix	403-418	16
β-strand	425-431	7	9
β-strand	442-451	10	9
α-helix	460-463	4
β-strand	471-475	5	9
α-helix	481-488	8
β-strand	496-499	4	8
β-strand	503	1	8
β-strand	511	1	10
β-strand	515-519	5	8
α-helix	522-524	3
β-strand	525-527	3	8
β-strand	536-548	13	11
β-strand	553-567	15	11
α-helix	572-574	3
α-helix	577-579	3
β-strand	581-586	6	11
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-612	4	11
α-helix	616-630	15
β-strand	634-637	4	11
α-helix	640-644	5
α-helix	645-654	10
α-helix	660-663	4
β-strand	666	1	10
α-helix	680-691	12
β-strand	695-698	4	11
α-helix	702-706	5
α-helix	716-724	9
α-helix	739-742	4
α-helix	744-767	24
α-helix	770-781	12
α-helix	785-790	6
α-helix	796-807	12
β-strand	810	1	9
α-helix	811-814	4
β-strand	849	1	12
β-strand	854-856	3	12
β-strand	860-864	5	12
α-helix	868-875	8
α-helix	896-898	3
α-helix	902-903	2
α-helix	905-926	22
α-helix	930-947	18
α-helix	951-955	5
α-helix	964-987	24
β-strand	991-995	5	12
β-strand	999-1003	5	12
α-helix	1009-1026	18
β-strand	1033-1045	13	12
β-strand	1048-1054	7	12
β-strand	1064-1069	6	12
α-helix	1072-1074	3
α-helix	1080-1093	14
α-helix	1099-1118	20
α-helix	1124-1127	4
β-strand	1129-1131	3	13
β-strand	1168-1172	5	13
β-strand	1173	1	14
β-strand	1193-1195	3	13
α-helix	1196-1200	5
α-helix	1202-1204	3
β-strand	1208	1	14
α-helix	1210-1214	5
α-helix	1215-1219	5
α-helix	1220-1225	6
α-helix	1234-1239	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha catalytic subunit A	A, B	protein	910	Saccharomyces cerevisiae	P13382 (AlphaFold model)
DNA (5'-d(tptptptpcpgpcptpgpcpcpcpgpcpcpt)-3')	C, D	DNA	16
RNA (5'-r(apgpgpcpgpgpgpcpapg)-3')	E, F	RNA	10

Sequence of entity 1 (A, B), FASTA

>4FXD_1 DNA polymerase alpha catalytic subunit A (chains A, B)
TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHE
EIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSS
DTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPT
TTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRP
PQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVL
AHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLT
PKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRI
QLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQN
EENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKE
DIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTAN
SMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDN
YADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEV
KGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYK
INMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALS
VAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKY
FRREGGNNNG

Sequence of entity 2 (C, D), FASTA

>4FXD_2 DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') (chains C, D)
TTTTCGCTGCCCGCCT

Sequence of entity 3 (E, F), FASTA

>4FXD_3 RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3') (chains E, F)
AGGCGGGCAG

Primary citation

Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha. Perera, R.L., Torella, R., Klinge, S. et al. Elife (2013) 2:e00482. DOI 10.7554/eLife.00482 · 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.
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…
8B9C 4.6 Å, S. cerevisiae pol alpha - replisome complex

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