5IUD: DNA polymerase alpha catalytic subunit

Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer. Determined by X-ray diffraction at 3.3 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 28,207
Mol. weight: 456.06 kDa
Released: 13 Apr 2016

Explore 5IUD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IUD contains 172 α-helices and 145 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 A: 43 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	342-350	9	1
β-strand	359-367	9	1
β-strand	372-380	9	1
β-strand	385-391	7	2
β-strand	394-396	3	3
β-strand	403-407	5	3
α-helix	408	1
α-helix	410-416	7
α-helix	417-421	5
β-strand	431-438	8	2
β-strand	449-457	9	2
α-helix	462-465	4
β-strand	473-477	5	2
α-helix	483-490	8
β-strand	498-501	4	1
β-strand	505	1	1
β-strand	512	1	4
β-strand	516-520	5	1
α-helix	523-525	3
β-strand	526-529	4	1
α-helix	533-536	4
β-strand	537-546	10	5
β-strand	557-568	12	5
α-helix	573-575	3
β-strand	581-586	6	5
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-611	3	5
α-helix	615-629	15
β-strand	633-636	4	5
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	4
α-helix	670-672	3
α-helix	682-684	3
β-strand	689-692	4	5
α-helix	693-700	8
α-helix	708-714	7
α-helix	730-732	3
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-781	6
α-helix	784-798	15
β-strand	801	1	2
α-helix	803-807	5
β-strand	845	1	6
α-helix	846-847	2
β-strand	850-852	3	7
α-helix	855	1
β-strand	856-861	6	7
α-helix	864-872	9
α-helix	907-908	2
α-helix	910-928	19
α-helix	936-954	19
α-helix	958-961	4
α-helix	970-993	24
β-strand	997-1000	4	7
β-strand	1001	1	6
β-strand	1005-1009	5	7
α-helix	1015-1030	16
β-strand	1038-1051	14	7
β-strand	1054-1061	8	7
β-strand	1069-1075	7	7
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	8
α-helix	1143-1145	3
α-helix	1153-1163	11
β-strand	1174-1177	4	8
β-strand	1178-1179	2	9
β-strand	1180-1181	2	10
β-strand	1192-1193	2	9
α-helix	1195-1200	6
β-strand	1205-1206	2	10
α-helix	1208-1210	3
α-helix	1211-1215	5
α-helix	1216-1223	8
α-helix	1232-1239	8

Chain D: 44 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	11
β-strand	355-367	13	11
β-strand	372-380	9	11
β-strand	385-386	2	12
β-strand	388-391	4	12
β-strand	396	1	13
β-strand	403	1	13
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-424	3
β-strand	431-438	8	12
β-strand	449-457	9	12
α-helix	462-465	4
β-strand	473-477	5	12
α-helix	483-490	8
β-strand	498-502	5	11
β-strand	505	1	11
β-strand	512	1	14
β-strand	516-520	5	11
α-helix	523-525	3
β-strand	526-529	4	11
α-helix	533-536	4
β-strand	537-548	12	15
β-strand	555-568	14	15
α-helix	573-575	3
β-strand	581-586	6	15
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-611	3	15
α-helix	615-629	15
β-strand	633-636	4	15
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	14
α-helix	683-685	3
β-strand	689-692	4	15
α-helix	693-700	8
α-helix	708-711	4
α-helix	712-716	5
α-helix	725-728	4
α-helix	729-733	5
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-779	4
α-helix	784-798	15
β-strand	801	1	12
α-helix	803-806	4
α-helix	845-847	3
β-strand	850-852	3	16
β-strand	856-861	6	16
α-helix	864-872	9
α-helix	897-903	7
α-helix	907-908	2
α-helix	910-928	19
α-helix	936-960	25
α-helix	970-993	24
β-strand	998-1000	3	16
β-strand	1005-1009	5	16
α-helix	1015-1029	15
β-strand	1038-1051	14	16
β-strand	1054-1062	9	16
β-strand	1068-1075	8	16
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1132	3
β-strand	1135-1138	4	17
α-helix	1153-1161	9
α-helix	1167-1169	3
β-strand	1174-1177	4	17
β-strand	1178-1179	2	18
β-strand	1180-1181	2	19
β-strand	1192-1193	2	18
α-helix	1195-1198	4
β-strand	1205-1206	2	19
α-helix	1208-1210	3
α-helix	1211-1215	5
α-helix	1216-1223	8
α-helix	1232-1239	8
α-helix	1243-1245	3

Chain G: 45 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	20
β-strand	355-367	13	20
β-strand	372-380	9	20
β-strand	385-391	7	21
β-strand	396	1	22
β-strand	403	1	22
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-424	3
β-strand	430-438	9	21
β-strand	449-457	9	21
α-helix	462-465	4
β-strand	473-477	5	21
α-helix	483-490	8
β-strand	498-502	5	20
α-helix	504	1
β-strand	505	1	20
α-helix	506-507	2
β-strand	512	1	23
β-strand	516-520	5	20
α-helix	523-525	3
β-strand	526-529	4	20
α-helix	533-536	4
β-strand	537-548	12	24
β-strand	555-568	14	24
α-helix	573-575	3
β-strand	581-586	6	24
α-helix	594-595	2
α-helix	598-605	8
β-strand	610-611	2	24
α-helix	615-629	15
β-strand	633-636	4	24
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	23
α-helix	679-682	4
β-strand	689-692	4	24
α-helix	693-700	8
α-helix	708-715	8
α-helix	719-721	3
α-helix	725-728	4
α-helix	730-732	3
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-781	6
α-helix	784-798	15
β-strand	801	1	21
α-helix	803-807	5
α-helix	845-847	3
β-strand	850-852	3	25
β-strand	856-861	6	25
α-helix	864-872	9
α-helix	898-901	4
α-helix	907-908	2
α-helix	910-928	19
α-helix	936-953	18
α-helix	956-960	5
α-helix	970-993	24
β-strand	998	1	25
β-strand	1005-1009	5	25
α-helix	1015-1030	16
β-strand	1038-1051	14	25
β-strand	1054-1062	9	25
β-strand	1068-1075	8	25
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1132	3
β-strand	1135-1138	4	26
α-helix	1153-1162	10
β-strand	1174-1177	4	26
β-strand	1178-1179	2	27
β-strand	1180	1	28
β-strand	1192-1193	2	27
α-helix	1195-1200	6
β-strand	1206	1	28
α-helix	1208-1210	3
α-helix	1211-1215	5
α-helix	1217-1223	7
α-helix	1234-1237	4

Chain J: 40 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	340-350	11	29
β-strand	359-366	8	29
β-strand	373-380	8	29
α-helix	384	1
β-strand	385-391	7	30
β-strand	394	1	31
β-strand	398	1	32
β-strand	401	1	32
β-strand	407	1	31
α-helix	408	1
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-424	3
β-strand	431-438	8	30
β-strand	449-457	9	30
α-helix	462-465	4
β-strand	473-477	5	30
α-helix	483-490	8
β-strand	498-502	5	29
β-strand	505	1	29
β-strand	512	1	33
β-strand	516-520	5	29
α-helix	523-525	3
β-strand	526-529	4	29
α-helix	533-536	4
β-strand	537-548	12	34
α-helix	549	1
β-strand	555-568	14	34
α-helix	573-575	3
β-strand	581-586	6	34
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-611	3	34
α-helix	615-629	15
β-strand	633-636	4	34
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	33
β-strand	689-692	4	34
α-helix	693-700	8
α-helix	708-715	8
α-helix	729-732	4
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-780	5
α-helix	785-798	14
β-strand	801	1	30
α-helix	803-807	5
α-helix	845-847	3
β-strand	850-852	3	35
β-strand	856-861	6	35
α-helix	864-871	8
α-helix	907-908	2
α-helix	910-928	19
α-helix	936-958	23
α-helix	970-993	24
β-strand	997-1000	4	35
β-strand	1005-1009	5	35
α-helix	1015-1030	16
β-strand	1038-1051	14	35
β-strand	1054-1062	9	35
β-strand	1068-1075	8	35
α-helix	1086-1100	15
α-helix	1105-1122	18
α-helix	1130-1132	3
β-strand	1135-1138	4	36
α-helix	1153-1163	11
β-strand	1174-1177	4	36
β-strand	1178-1179	2	37
β-strand	1180	1	38
β-strand	1192-1193	2	37
α-helix	1195-1200	6
β-strand	1206	1	38
α-helix	1208-1213	6
α-helix	1216-1223	8
α-helix	1232-1239	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha catalytic subunit	A, D, G, J	protein	918	Homo sapiens	P09884 (AlphaFold model)
DNA template	B, E, H, K	DNA	16	Homo sapiens
DNA primer	C, F, I, L	DNA	13	Homo sapiens

Sequence of entity 1 (A, D, G, J), FASTA

>5IUD_1 DNA polymerase alpha catalytic subunit (chains A, D, G, J)
EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKID
LNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKY
SAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKVE
AMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKP
PFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISA
KELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMC
ELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLG
DEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFT
TVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPD
LILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE
VIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAA
LVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLI
EIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSY
VICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIAT
WLGLDPTQFRVHHYHKDE

Sequence of entity 2 (B, E, H, K), FASTA

>5IUD_2 DNA template (chains B, E, H, K)
ATGGTAGGGGAAGGAT

Sequence of entity 3 (C, F, I, L), FASTA

>5IUD_3 DNA primer (chains C, F, I, L)
ATCCTTCCCCTAC

Primary citation

Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer. Coloma, J., Johnson, R.E., Prakash, L. et al. Sci Rep (2016) 6:23784-23784. DOI 10.1038/srep23784 · PubMed

Other PDB entries of the same protein (UniProt P09884 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QCL 2.2 Å, Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex…
4Y97 2.51 Å, Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of…
4Q5V 2.52 Å, Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex…
7N2M 2.9 Å, Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and…
6AS7 2.95 Å, Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex…
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
8D96 3.35 Å, Human DNA polymerase alpha/primase elongation complex I bound to primer/template
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…
9MJ5 3.5 Å, Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA

Browse structure collections

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