9MJ5: Catalytic domain of human DNA polymerase alpha

Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA. Determined by electron microscopy at 3.5 Å resolution. Released 19 Feb 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,919
Mol. weight: 179.33 kDa
Ligands: ZN, MG, DCP
Released: 19 Feb 2025

Explore 9MJ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MJ5 contains 60 α-helices and 68 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10-11	2	1
α-helix	14-19	6
β-strand	21	1	1
β-strand	24-34	11	1
β-strand	40-44	5	1
β-strand	50-54	5	1
β-strand	66-73	8	1
β-strand	79-80	2	1
β-strand	83-86	4	1
α-helix	87-88	2
α-helix	96-108	13
α-helix	110-112	3

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	46-48	3	2
α-helix	51-56	6
β-strand	58-60	3	3
β-strand	63-66	4	3
β-strand	69-70	2	3
β-strand	73-85	13	2
β-strand	89-95	7	2
β-strand	102-107	6	2
α-helix	116-118	3
α-helix	119-121	3
β-strand	125-135	11	2
β-strand	138-148	11	2
α-helix	154-174	21
α-helix	207-218	12
β-strand	225	1	4
α-helix	227-233	7
α-helix	239-252	14
β-strand	255-256	2	5
β-strand	264	1	4
β-strand	265-266	2	5

Chain C: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	445-451	7
β-strand	460-471	12	6
β-strand	477-480	4	7
α-helix	481	1
α-helix	488	1
β-strand	489	1	7
α-helix	490	1
β-strand	491-492	2	8
β-strand	498-500	3	8
β-strand	505-507	3	8
β-strand	511-514	4	7
β-strand	517-521	5	6
β-strand	526-530	5	6
α-helix	533-540	8
α-helix	544-553	10
α-helix	555-564	10
β-strand	569-580	12	6
β-strand	585-596	12	6
α-helix	600-615	16

Chain S: 40 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	340-349	10	9
β-strand	359-367	9	9
β-strand	372-380	9	9
β-strand	384-391	8	10
β-strand	394-396	3	11
β-strand	403-407	5	11
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-425	4
β-strand	431-438	8	10
β-strand	449-458	10	10
β-strand	473-477	5	10
α-helix	483-491	9
β-strand	498-502	5	9
β-strand	505	1	9
β-strand	512	1	12
β-strand	516-520	5	9
β-strand	526-528	3	9
α-helix	533-536	4
β-strand	537-548	12	13
β-strand	555-568	14	13
α-helix	573-575	3
β-strand	581-586	6	13
α-helix	592-595	4
α-helix	598-605	8
β-strand	609-611	3	13
α-helix	615-629	15
β-strand	633-636	4	13
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	12
α-helix	670-672	3
α-helix	679-684	6
β-strand	689-692	4	13
α-helix	693-700	8
α-helix	708-715	8
α-helix	727-730	4
α-helix	735-759	25
α-helix	761-772	12
α-helix	776-781	6
α-helix	785-798	14
α-helix	803-807	5
β-strand	844	1	14
α-helix	845-847	3
β-strand	850-852	3	15
β-strand	856-861	6	15
α-helix	864-872	9
α-helix	900-903	4
α-helix	910-930	21
α-helix	936-958	23
α-helix	959-961	3
α-helix	971-993	23
β-strand	997-1000	4	15
β-strand	1002	1	14
β-strand	1005-1009	5	15
α-helix	1015-1030	16
β-strand	1038-1051	14	15
β-strand	1054-1062	9	15
β-strand	1068-1075	8	15
α-helix	1086-1100	15
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	16
α-helix	1143-1145	3
α-helix	1153-1164	12
β-strand	1174-1177	4	16
β-strand	1178-1179	2	17
β-strand	1180	1	18
α-helix	1188-1190	3
β-strand	1192-1193	2	17
α-helix	1195-1200	6
β-strand	1206	1	18
α-helix	1208-1214	7
α-helix	1217-1223	7
α-helix	1232-1238	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replication protein A 14 kDa subunit	A	protein	121	Homo sapiens	P35244 (AlphaFold model)
Replication protein A 32 kDa subunit	B	protein	236	Homo sapiens	P15927 (AlphaFold model)
Replication protein A 70 kDa DNA-binding subunit	C	protein	179	Homo sapiens	P27694 (AlphaFold model)
RNA-DNA primer (11-mer)	P	NA-hybrid	11	Homo sapiens
DNA polymerase alpha catalytic subunit	S	protein	910	Homo sapiens	P09884 (AlphaFold model)
DNA template (35-mer)	T	DNA	35	Homo sapiens

Sequence of entity 1 (A), FASTA

>9MJ5_1 Replication protein A 14 kDa subunit (chains A)
MVDMMDLPRSRINAGMLAQFIDKPVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLD
EEISGIVEVVGRVTAKATILCTSYVQFKEDSHPFDLGLYNEAVKIIHDFPQFYPLGIVQH
D

Sequence of entity 2 (B), FASTA

>9MJ5_2 Replication protein A 32 kDa subunit (chains B)
AEKKSRARAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKI
DDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNE
FTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLN
LIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE

Sequence of entity 3 (C), FASTA

>9MJ5_3 Replication protein A 70 kDa DNA-binding subunit (chains C)
SNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPTQDCNKKVIDQQNGL
YRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDKNEQA
FEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRRSALM

Sequence of entity 4 (P), FASTA

>9MJ5_4 RNA-DNA primer (11-mer) (chains P)
GCCUGGAGCGC

Sequence of entity 5 (S), FASTA

>9MJ5_5 DNA polymerase alpha catalytic subunit (chains S)
ADEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREM
KIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLE
VKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWC
KVEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAA
PKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDII
VGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVE
ISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQ
IMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQ
KLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNI
CFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDL
NPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM
NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKK
YAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK
RLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDT
VSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVL
IATWLGLDPT

Sequence of entity 6 (T), FASTA

>9MJ5_6 DNA template (35-mer) (chains T)
AATCTAGTAACATAGTATACATAGGCGCTCCAGGC

Ligands and cofactors

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

Primary citation

The human primosome requires replication protein A when copying DNA with inverted repeats. Baranovskiy, A.G., Morstadt, L.M., Romero, E.E. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf799 · PubMed

Other PDB entries of the same protein (UniProt P35244 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KDF 1.98 Å, X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell…
2PI2 2.0 Å, Full-length Replication protein A subunits RPA14 and RPA32
1QUQ 2.5 Å, Complex of replication protein A subunits RPA14 and RPA32
2PQA 2.5 Å, Crystal Structure of Full-length Human RPA 14/32 Heterodimer
1L1O 2.8 Å, Structure of the human Replication Protein A (RPA) trimerization core
2Z6K 3.0 Å, Crystal structure of full-length human RPA14/32 heterodimer
8RK2 3.2 Å, Human Replication protein A (RPA; trimeric core) - ssDNA complex
9PD3 3.3 Å, NER dual incision complex - DuIS
9PD4 3.4 Å, NER dual incision complex - DuIM
9A1V Integrative model of Nucleotide excision repair complex of XPA and RPA on 5' junction…
9A1Y Integrative model of Nucleotide excision repair complex of XPA and RPA on 3' junction…
9A88 Structure of the pre-incision complex in nucleotide excision repair

Browse structure collections

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