3FLO: DNA polymerase alpha subunit B

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit. Determined by X-ray diffraction at 2.5 Å resolution. Released 9 Jun 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 20,656
Mol. weight: 311.63 kDa
Ligands: ZN
Released: 9 Jun 2009

Explore 3FLO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FLO contains 139 α-helices and 180 β-strands across 12 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.

Chains A, C and E: 24 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	254-276	23
α-helix	280-282	3
β-strand	283	1	1
β-strand	294-302	9	1
β-strand	316-319	4	1
α-helix	320-321	2
α-helix	322-325	4
β-strand	329-333	5	1
β-strand	340-342	3	2
β-strand	347-353	7	1
β-strand	360-365	6	1
α-helix	367-374	8
β-strand	375-377	3	3
α-helix	378-388	11
β-strand	393-399	7	4
α-helix	411-419	9
α-helix	420-424	5
β-strand	428-432	5	4
β-strand	437	1	5
α-helix	441-445	5
α-helix	461-468	8
α-helix	470-473	4
β-strand	481-485	5	4
β-strand	490	1	5
β-strand	498	1	6
β-strand	500	1	7
α-helix	501-503	3
β-strand	515-517	3	4
β-strand	520	1	7
β-strand	522-526	5	8
β-strand	529-533	5	8
α-helix	538-541	4
β-strand	545-547	3	2
α-helix	549-553	5
α-helix	556-567	12
β-strand	569	1	9
α-helix	576-577	2
β-strand	578-579	2	10
β-strand	608-609	2	10
β-strand	612	1	6
α-helix	614-620	7
β-strand	621	1	9
α-helix	622	1
α-helix	623-625	3
α-helix	626-628	3
β-strand	630-632	3	8
α-helix	638-639	2
β-strand	640-644	5	8
β-strand	647-651	5	8
β-strand	656	1	11
β-strand	662	1	11
β-strand	664-670	7	4
α-helix	671-673	3
β-strand	681-683	3	3
α-helix	684	1
β-strand	689-691	3	3
α-helix	694-697	4
β-strand	698-704	7	4

Chain B: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1283-1286	4	13
β-strand	1293-1296	4	13
β-strand	1305-1308	4	14
β-strand	1311-1314	4	14
α-helix	1319	1
β-strand	1320	1	14
α-helix	1321-1322	2
α-helix	1323-1343	21
β-strand	1346-1348	3	15
β-strand	1356-1357	2	15
β-strand	1366	1	16
α-helix	1374	1
β-strand	1375	1	16
β-strand	1376-1378	3	15
α-helix	1382-1395	14
α-helix	1398-1402	5
α-helix	1407-1408	2
α-helix	1421-1423	3
α-helix	1424-1433	10
α-helix	1435-1449	15

Chain D: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1282-1283	2
β-strand	1284-1286	3	29
β-strand	1293-1295	3	29
β-strand	1305-1308	4	30
β-strand	1311-1314	4	30
α-helix	1319	1
β-strand	1320	1	30
α-helix	1321-1322	2
α-helix	1323-1342	20
β-strand	1346-1348	3	31
β-strand	1356-1357	2	31
β-strand	1366	1	32
α-helix	1374	1
β-strand	1375	1	32
β-strand	1376-1378	3	31
α-helix	1382-1395	14
α-helix	1398-1402	5
α-helix	1407-1408	2
α-helix	1421-1423	3
α-helix	1424-1433	10
α-helix	1435-1449	15

Chain F: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1282	1
β-strand	1283-1286	4	43
β-strand	1293-1296	4	43
β-strand	1305-1308	4	44
β-strand	1311-1314	4	44
α-helix	1319	1
β-strand	1320	1	44
α-helix	1321-1322	2
α-helix	1323-1343	21
β-strand	1346-1348	3	45
β-strand	1356-1357	2	45
β-strand	1366	1	46
α-helix	1374	1
β-strand	1375	1	46
β-strand	1376-1378	3	45
α-helix	1382-1395	14
α-helix	1398-1402	5
α-helix	1407-1408	2
α-helix	1424-1433	10
α-helix	1435-1451	17

Chain G: 25 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	254-275	22
α-helix	280-282	3
β-strand	283	1	47
β-strand	294-302	9	47
β-strand	316-319	4	47
α-helix	320-321	2
α-helix	322-325	4
β-strand	329-333	5	47
β-strand	340-342	3	48
β-strand	347-353	7	47
β-strand	360-365	6	47
α-helix	367-374	8
β-strand	375-376	2	49
α-helix	378-388	11
β-strand	393-399	7	50
α-helix	411-419	9
α-helix	420-424	5
β-strand	428-432	5	50
β-strand	437	1	51
α-helix	441-445	5
α-helix	461-468	8
α-helix	470-473	4
β-strand	481-485	5	50
β-strand	490	1	51
β-strand	498	1	52
β-strand	500	1	53
α-helix	501-503	3
α-helix	505-508	4
β-strand	515-517	3	50
β-strand	520	1	53
β-strand	522-526	5	28
β-strand	529-533	5	28
α-helix	538-541	4
β-strand	545-547	3	48
α-helix	549-553	5
α-helix	556-567	12
β-strand	569	1	54
α-helix	576-577	2
β-strand	578-579	2	55
β-strand	608-609	2	55
β-strand	612	1	52
α-helix	614-620	7
β-strand	621	1	54
α-helix	622	1
α-helix	623-625	3
α-helix	626-628	3
β-strand	630-632	3	28
α-helix	638-639	2
β-strand	640-644	5	28
β-strand	647-651	5	28
β-strand	656	1	56
β-strand	662	1	56
β-strand	664-670	7	50
α-helix	671-673	3
β-strand	681-683	3	49
α-helix	684	1
β-strand	689-691	3	49
α-helix	694-697	4
β-strand	698-704	7	50

Chain H: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1275-1277	3
β-strand	1284-1286	3	57
β-strand	1293-1295	3	57
β-strand	1305-1308	4	58
β-strand	1311-1314	4	58
α-helix	1319	1
β-strand	1320	1	58
α-helix	1321-1322	2
α-helix	1323-1343	21
β-strand	1346-1348	3	59
β-strand	1356-1357	2	59
β-strand	1366	1	60
α-helix	1374	1
β-strand	1375	1	60
β-strand	1376-1378	3	59
α-helix	1382-1395	14
α-helix	1398-1402	5
α-helix	1407-1408	2
α-helix	1421-1423	3
α-helix	1424-1433	10
α-helix	1435-1450	16

Chains I, J, K and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1001	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha subunit B	A, C, E, G	protein	460	Saccharomyces cerevisiae	P38121 (AlphaFold model)
DNA polymerase alpha catalytic subunit A	I, J, K, L	protein	3	Saccharomyces cerevisiae
DNA polymerase alpha catalytic subunit A	B, D, F, H	protein	206	Saccharomyces cerevisiae	P13382 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3FLO_1 DNA polymerase alpha subunit B (chains A, C, E, G)
KFRTMRQNLQEASDVLDDQIESFTKIIQNHYKLSPNDFADPTIQSQSEIYAVGRIVPDSP
TYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAFKGKNANGDYFTVNSI
LPLPYPNSPVSTSQELQEFQANLEGSSLKVIVTCGPYFANDNFSLELLQEFIDSINNEVK
PHVLIMFGPFIDITHPLIASGKLPNFPQFKTQPKTLDELFLKLFTPILKTISPHIQTVLI
PSTKDAISNHAAYPQASLIRKALQLPKRNFKCMANPSSFQINEIYFGCSNVDTFKDLKEV
IKGGTTSSRYRLDRVSEHILQQRRYYPIFPGSIRTRIKPKDVSTKKETNDMESKEEKVYE
HISGADLDVSYLGLTEFVGGFSPDIMIIPSELQHFARVVQNVVVINPGRFIRATGNRGSY
AQITVQCPDLEDGKLTLVEGEEPVYLHNVWKRARVDLIAS

Sequence of entity 2 (I, J, K, L), FASTA

>3FLO_2 DNA polymerase alpha catalytic subunit A (chains I, J, K, L)
XXX

Sequence of entity 3 (B, D, F, H), FASTA

>3FLO_3 DNA polymerase alpha catalytic subunit A (chains B, D, F, H)
NLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQLFT
PLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGCTGVMRYKYSD
KQLYNQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGR
SVVQKYLNDCGRRYVDMTSIFDFMLN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (SO4) are not listed.

Primary citation

3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. Klinge, S., Nunez-Ramirez, R., Llorca, O. et al. EMBO J (2009) 28:1978-1987. DOI 10.1038/emboj.2009.150 · PubMed

Other PDB entries of the same protein (UniProt P38121 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
8FOH 4.6 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the RNA…
8FOJ 4.8 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the post RNA…
8FOE 5.6 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex bound to a…

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