4QCL: 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 dCTP. Determined by X-ray diffraction at 2.2 Å resolution. Released 26 Nov 2014.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,910
Mol. weight: 116.56 kDa
Ligands: DCP, MG, ZN
Released: 26 Nov 2014

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

Secondary structure: helices and β-sheets

4QCL contains 48 α-helices and 37 β-strands across 1 chain. 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: 48 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
α-helix	383-384	2
β-strand	385-391	7	2
α-helix	392	1
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	483-491	9
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	670-671	2
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	725-732	8
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-779	4
α-helix	785-798	14
β-strand	801	1	2
α-helix	804-806	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	910-930	21
α-helix	936-960	25
α-helix	970-993	24
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	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	8
α-helix	1143-1145	3
α-helix	1149-1151	3
α-helix	1153-1164	12
β-strand	1174-1177	4	8
β-strand	1178-1179	2	9
β-strand	1180-1181	2	10
α-helix	1188-1190	3
β-strand	1192-1193	2	9
α-helix	1195-1200	6
β-strand	1205-1206	2	10
α-helix	1208-1211	4
α-helix	1212-1216	5
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	protein	922	Homo sapiens	P09884 (AlphaFold model)
RNA primer	B	NA-hybrid	11
DNA template	C	DNA	21

Sequence of entity 1 (A), FASTA

>4QCL_1 DNA polymerase alpha catalytic subunit (chains A)
DEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMK
IDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEV
KYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCK
AEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAP
KPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIV
GHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEI
SAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQI
MCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQK
LGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNIC
FTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLN
PDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMN
LEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKY
AALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKR
LIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTV
SYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLI
ATWLGLDPTQFRVHHYHKDEEN

Sequence of entity 2 (B), FASTA

>4QCL_2 RNA PRIMER (chains B)
GCCUGGAGCGC

Sequence of entity 3 (C), FASTA

>4QCL_3 DNA TEMPLATE (chains C)
ATTACTATAGGCGCTCCAGGC

Ligands and cofactors

ID	Name	Formula	Copies
DCP	2'-deoxycytidine-5'-triphosphate	C9 H16 N3 O13 P3	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	3

Water and common crystallization additives (K, 1PE, EDO) are not listed.

Primary citation

Activity and fidelity of human DNA polymerase alpha depend on primer structure. Baranovskiy, A.G., Duong, V., Babayeva, N.D. et al. J Biol Chem (2018).

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

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
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

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