4Y97: Human Pol alpha B-subunit

Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit. Determined by X-ray diffraction at 2.51 Å resolution. Released 15 Apr 2015.

Method: X-ray diffraction
Resolution: 2.51 Å
Organism: Homo sapiens
Chains: 8
Atoms: 19,724
Mol. weight: 349.35 kDa
Ligands: ZN
Released: 15 Apr 2015

Explore 4Y97 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y97 contains 129 α-helices and 174 β-strands across 8 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: 22 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-175	6	1
β-strand	193-195	3	2
α-helix	213-234	22
α-helix	240-242	3
β-strand	251-259	9	3
β-strand	270-274	5	3
α-helix	275	1
α-helix	276-279	4
β-strand	283-287	5	3
β-strand	294-296	3	4
β-strand	301-307	7	3
β-strand	314-319	6	3
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	5
α-helix	328	1
α-helix	333-336	4
β-strand	340-346	7	1
α-helix	358-370	13
β-strand	374-378	5	1
β-strand	383	1	6
α-helix	387-390	4
α-helix	398-412	15
α-helix	414-416	3
α-helix	418	1
β-strand	419-423	5	1
β-strand	428	1	6
β-strand	435	1	7
β-strand	437	1	8
α-helix	438-440	3
α-helix	449-451	3
β-strand	453-455	3	1
β-strand	458	1	8
β-strand	460-464	5	2
β-strand	467-471	5	2
α-helix	476-481	6
β-strand	485-487	3	4
α-helix	494-505	12
β-strand	507	1	9
α-helix	514-515	2
β-strand	520	1	7
α-helix	522-528	7
β-strand	530	1	9
β-strand	534	1	5
β-strand	537-539	3	2
α-helix	545-546	2
β-strand	547-551	5	2
β-strand	554-558	5	2
β-strand	563-564	2	10
β-strand	567-568	2	10
β-strand	570-576	7	1
α-helix	578-580	3
β-strand	590-597	8	1

Chains B and F: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279-1282	4	11
α-helix	1288	1
β-strand	1289-1292	4	11
β-strand	1296-1297	2	12
β-strand	1304-1305	2	12
α-helix	1319-1322	4
α-helix	1323-1342	20
β-strand	1346-1348	3	13
β-strand	1356-1357	2	13
β-strand	1364-1365	2	14
β-strand	1368-1369	2	14
β-strand	1370	1	15
α-helix	1371	1
β-strand	1378	1	15
β-strand	1379-1381	3	13
α-helix	1385-1397	13
α-helix	1401-1406	6
α-helix	1411-1420	10
α-helix	1424-1434	11

Chain C: 21 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-175	6	16
β-strand	193-195	3	17
α-helix	213-234	22
α-helix	240-242	3
β-strand	251-259	9	18
β-strand	270-274	5	18
α-helix	275	1
α-helix	276-279	4
β-strand	283-287	5	18
β-strand	295-296	2	19
β-strand	301-307	7	18
β-strand	314-319	6	18
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	20
α-helix	328	1
α-helix	333-336	4
β-strand	340-346	7	16
α-helix	358-370	13
β-strand	374-378	5	16
β-strand	383	1	21
α-helix	387-390	4
α-helix	398-412	15
α-helix	414-416	3
α-helix	418	1
β-strand	419-423	5	16
β-strand	428	1	21
β-strand	435	1	22
β-strand	437	1	23
α-helix	438-440	3
β-strand	444	1	24
α-helix	449-451	3
β-strand	453-455	3	16
β-strand	458	1	23
β-strand	460-464	5	17
β-strand	467-471	5	17
α-helix	476-481	6
β-strand	485-486	2	19
α-helix	494-505	12
β-strand	507	1	25
α-helix	514-515	2
β-strand	520	1	22
α-helix	522-528	7
β-strand	530	1	25
β-strand	534	1	20
β-strand	537-539	3	17
α-helix	545-546	2
β-strand	547-551	5	17
β-strand	554-558	5	17
β-strand	563-564	2	26
β-strand	567-568	2	26
β-strand	570-576	7	16
β-strand	590-597	8	16

Chains D and H: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279-1282	4	27
α-helix	1288	1
β-strand	1289-1292	4	27
β-strand	1296-1297	2	28
β-strand	1304-1305	2	28
α-helix	1319-1322	4
α-helix	1323-1342	20
β-strand	1346-1348	3	29
β-strand	1356-1357	2	29
β-strand	1364-1365	2	30
β-strand	1368-1369	2	30
β-strand	1370	1	31
α-helix	1371	1
β-strand	1378	1	31
β-strand	1379-1381	3	29
α-helix	1385-1397	13
α-helix	1401-1406	6
α-helix	1411-1420	10
α-helix	1424-1434	11
α-helix	1436-1439	4

Chain E: 22 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-175	6	32
β-strand	193-196	4	33
α-helix	213-234	22
α-helix	240-242	3
β-strand	251-259	9	34
β-strand	270-274	5	34
α-helix	275	1
α-helix	276-279	4
β-strand	283-287	5	34
β-strand	295-296	2	35
β-strand	301-307	7	34
β-strand	314-319	6	34
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	36
α-helix	328	1
α-helix	333-336	4
β-strand	340-346	7	32
α-helix	358-370	13
β-strand	374-378	5	32
β-strand	383	1	37
α-helix	387-390	4
α-helix	398-412	15
α-helix	414-416	3
α-helix	418	1
β-strand	419-423	5	32
β-strand	428	1	37
β-strand	435	1	38
β-strand	437	1	39
α-helix	438-440	3
β-strand	444	1	24
α-helix	449-451	3
β-strand	453-455	3	32
β-strand	458	1	39
β-strand	460-464	5	33
β-strand	467-471	5	33
α-helix	476-481	6
β-strand	485-486	2	35
α-helix	494-505	12
β-strand	507	1	40
α-helix	514-515	2
β-strand	520	1	38
α-helix	522-528	7
β-strand	530	1	40
β-strand	534	1	36
β-strand	537-539	3	33
α-helix	545-546	2
β-strand	547-551	5	33
β-strand	554-558	5	33
β-strand	563-564	2	41
β-strand	567-568	2	41
β-strand	570-576	7	32
α-helix	578-580	3
β-strand	590-597	8	32

Chain G: 22 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-175	6	47
β-strand	193-195	3	48
α-helix	213-234	22
α-helix	240-242	3
β-strand	251-259	9	49
β-strand	270-274	5	49
α-helix	275	1
α-helix	276-279	4
β-strand	283-287	5	49
β-strand	295-296	2	50
β-strand	301-307	7	49
β-strand	314-319	6	49
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	51
α-helix	328	1
α-helix	333-336	4
β-strand	340-346	7	47
α-helix	358-370	13
β-strand	374-378	5	47
β-strand	383	1	52
α-helix	387-390	4
α-helix	398-412	15
α-helix	414-416	3
α-helix	418	1
β-strand	419-423	5	47
β-strand	428	1	52
β-strand	435	1	53
β-strand	437	1	54
α-helix	438-440	3
α-helix	449-452	4
β-strand	453-455	3	47
β-strand	458	1	54
β-strand	460-464	5	48
β-strand	467-471	5	48
α-helix	476-481	6
β-strand	485-486	2	50
α-helix	494-505	12
β-strand	507	1	55
α-helix	514-515	2
β-strand	520	1	53
α-helix	522-528	7
β-strand	530	1	55
β-strand	534	1	51
β-strand	537-539	3	48
α-helix	545-546	2
β-strand	547-551	5	48
β-strand	554-558	5	48
β-strand	563-564	2	56
β-strand	567-568	2	56
β-strand	570-576	7	47
α-helix	578-580	3
β-strand	590-597	8	47

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha subunit B	A, C, E, G	protein	598	Homo sapiens	Q14181 (AlphaFold model)
DNA polymerase alpha catalytic subunit	B, D, F, H	protein	180	Homo sapiens	P09884 (AlphaFold model)

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

>4Y97_1 DNA polymerase alpha subunit B (chains A, C, E, G)
MSASAQQLAEELQIFGLDCEEALIEKLVELCVQYGQNEEGMVGELIAFCTSTHKVGLTSE
ILNSFEHEFLSKRLSKARHSTCKDSGHAGARDIVSIQELIEVEEEEEILLNSYTTPSKGS
QKRAISTPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQKYNSRSNRGEVVTSFGLAQGV
SWSGRGGAGNISLKVLGCPEALTGSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIEAF
TPLLAPAQEPVTLLGQIGCDSNGKLNNKSVILEGDREHSSGAQIPVDLSELKEYSLFPGQ
VVIMEGINTTGRKLVATKLYEGVPLPFYQPTEEDADFEQSMVLVACGPYTTSDSITYDPL
LDLIAVINHDRPDVCILFGPFLDAKHEQVENCLLTSPFEDIFKQCLRTIIEGTRSSGSHL
VFVPSLRDVHHEPVYPQPPFSYSDLSREDKKQVQFVSEPCSLSINGVIFGLTSTDLLFHL
GAEEISSSSGTSDRFSRILKHILTQRSYYPLYPPQEDMAIDYESFYVYAQLPVTPDVLII
PSELRYFVKDVLGCVCVNPGRLTKGQVGGTFARLYLRRPAADGAERQSPCIAVQVVRI

Sequence of entity 2 (B, D, F, H), FASTA

>4Y97_2 DNA polymerase alpha catalytic subunit (chains B, D, F, H)
AQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGSGTDMEPSLYRCSNIDCKASPLTFTV
QLSNKLIMDIRRFIKKYYDGWLICEEPTCRNRTRHLPLQFSRTGPLCPACMKATLQPEYS
DKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFTPKVLQDYRKLKNTAEQFLSRS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Crystal Structure of the Human Pol alpha B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit. Suwa, Y., Gu, J., Baranovskiy, A.G. et al. J Biol Chem (2015) 290:14328-14337. DOI 10.1074/jbc.M115.649954 · PubMed

Other PDB entries of the same protein (UniProt Q14181 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VY3 2.98 Å, Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)
8QJ7 3.07 Å, Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1
9C8V 3.39 Å, Human DNA polymerase alpha/primase - CHAPSO (4 mM)
8B9D 3.4 Å, Human replisome bound by Pol Alpha
8D0B 3.43 Å, Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback…
8D9D 3.59 Å, Human DNA polymerase-alpha/primase elongation complex II bound to primer/template
5EXR 3.6 Å, Crystal structure of human primosome
7OPL 4.12 Å, CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1
8D0K 4.27 Å, Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback…
7U5C 4.6 Å, Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment…
4E2I 5.0 Å, The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA…
2KEB NMR solution structure of the N-terminal domain of the DNA polymerase alpha p68 subunit

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