4Q5V: DNA polymerase alpha catalytic subunit

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin. Determined by X-ray diffraction at 2.52 Å resolution. Released 26 Nov 2014.

Method: X-ray diffraction
Resolution: 2.52 Å
Organism: Homo sapiens
Chains: 6
Atoms: 15,085
Mol. weight: 231.73 kDa
Ligands: 2ZE
Released: 26 Nov 2014

Explore 4Q5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q5V contains 89 α-helices and 75 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: 46 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	340-350	11	1
β-strand	359-367	9	1
α-helix	368-370	3
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	410-416	7
α-helix	417-421	5
α-helix	422-425	4
β-strand	431-438	8	2
β-strand	449-457	9	2
α-helix	463-465	3
β-strand	473-477	5	2
α-helix	483-490	8
β-strand	497-502	6	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	537-548	12	5
β-strand	555-568	14	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	644-653	10
α-helix	659-662	4
β-strand	665	1	4
α-helix	679-684	6
β-strand	689-692	4	5
α-helix	693-700	8
α-helix	708-711	4
α-helix	712-716	5
α-helix	725-731	7
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-779	4
α-helix	784-798	15
β-strand	801	1	2
α-helix	804-807	4
α-helix	835-837	3
β-strand	844	1	6
α-helix	845-847	3
β-strand	850-852	3	7
β-strand	856-861	6	7
α-helix	864-871	8
α-helix	898-903	6
α-helix	907-909	3
α-helix	910-929	20
α-helix	938-960	23
α-helix	970-992	23
β-strand	997-1000	4	7
β-strand	1002	1	6
β-strand	1005-1009	5	7
α-helix	1015-1030	16
β-strand	1038-1051	14	7
β-strand	1054-1062	9	7
β-strand	1068-1075	8	7
α-helix	1078-1080	3
α-helix	1086-1100	15
α-helix	1105-1125	21
β-strand	1135-1138	4	8
α-helix	1143-1145	3
α-helix	1149-1151	3
α-helix	1153-1164	12
β-strand	1174-1177	4	8
β-strand	1178-1179	2	9
β-strand	1180	1	10
α-helix	1188-1190	3
β-strand	1192-1193	2	9
α-helix	1195-1200	6
β-strand	1206	1	10
α-helix	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
α-helix	1232-1238	7

Chain E: 43 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	340-349	10	11
β-strand	359-367	9	11
α-helix	368-370	3
β-strand	372-380	9	11
β-strand	385-391	7	12
β-strand	394-397	4	13
β-strand	402-407	6	13
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-425	4
β-strand	431-436	6	12
β-strand	438	1	14
β-strand	451-457	7	12
β-strand	473-477	5	12
α-helix	483-491	9
β-strand	497-502	6	11
β-strand	505	1	11
β-strand	512	1	15
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	16
β-strand	555-568	14	16
α-helix	573-575	3
β-strand	581-586	6	16
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-611	3	16
α-helix	615-629	15
β-strand	633-636	4	16
α-helix	639-643	5
α-helix	644-653	10
α-helix	659-662	4
β-strand	665	1	15
α-helix	679-684	6
β-strand	689-692	4	16
α-helix	693-700	8
α-helix	708-711	4
α-helix	712-716	5
α-helix	725-730	6
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-780	5
α-helix	785-798	14
β-strand	801	1	14
α-helix	802-807	6
β-strand	844	1	17
α-helix	845-847	3
β-strand	850-852	3	18
β-strand	856-861	6	18
α-helix	864-871	8
α-helix	900-903	4
α-helix	907-909	3
α-helix	910-929	20
α-helix	938-960	23
α-helix	970-992	23
β-strand	997-1000	4	18
β-strand	1002	1	17
β-strand	1005-1009	5	18
α-helix	1015-1029	15
β-strand	1038-1051	14	18
β-strand	1054-1062	9	18
β-strand	1068-1075	8	18
α-helix	1078-1080	3
α-helix	1086-1100	15
α-helix	1105-1125	21
β-strand	1135-1138	4	19
α-helix	1149-1151	3
α-helix	1153-1164	12
β-strand	1174-1177	4	19
β-strand	1178-1179	2	20
β-strand	1180	1	21
α-helix	1188-1190	3
β-strand	1192-1193	2	20
α-helix	1195-1200	6
β-strand	1206	1	21
α-helix	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
α-helix	1232-1238	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha catalytic subunit	A, E	protein	922	Homo sapiens	P09884 (AlphaFold model)
RNA primer	B, F	RNA	11
DNA template	C, G	DNA	21

Sequence of entity 1 (A, E), FASTA

>4Q5V_1 DNA polymerase alpha catalytic subunit (chains A, E)
DEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMK
IDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEV
KYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCK
AEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAP
KPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIV
GHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEI
SAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQI
MCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQK
LGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNIC
FTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLN
PDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN
LEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKY
AALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKR
LIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTV
SYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLI
ATWLGLDPTQFRVHHYHKDEEN

Sequence of entity 2 (B, F), FASTA

>4Q5V_2 RNA primer (chains B, F)
GCCUGGAGCGC

Sequence of entity 3 (C, G), FASTA

>4Q5V_3 DNA template (chains C, G)
ATTACTATAGGCGCTCCAGGC

Ligands and cofactors

ID	Name	Formula	Copies
2ZE	(3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecah…	C20 H34 O4	2

Primary citation

Structural basis for inhibition of DNA replication by aphidicolin. Baranovskiy, A.G., Babayeva, N.D., Suwa, Y. et al. Nucleic Acids Res (2014) 42:14013-14021. DOI 10.1093/nar/gku1209 · 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…
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
5IUD 3.3 Å, Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer
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

About this viewer

MolViewer shows 4Q5V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.