7N2M: DNA polymerase alpha catalytic core

Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and template/primer having T-C mismatch at the post-insertion site. Determined by X-ray diffraction at 2.9 Å resolution. Released 20 Apr 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,606
Mol. weight: 114.82 kDa
Ligands: DCP, MG, ZN
Released: 20 Apr 2022

Explore 7N2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2M contains 45 α-helices and 39 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: 45 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	340-350	11	1
β-strand	359-367	9	1
β-strand	372-380	9	1
β-strand	385-391	7	2
β-strand	394-397	4	3
β-strand	402-407	6	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	725-733	9
α-helix	735-759	25
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	899-903	5
α-helix	910-930	21
α-helix	936-958	23
α-helix	959-961	3
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	1105-1124	20
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	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
β-strand	1228	1	11
β-strand	1230	1	11
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 (5'-r(gpcpcpupgpgpapgpcpgp*c)-3')	B	RNA	11	Homo sapiens
DNA (5'-d(aptapgptpcpgpcptpcpcpapgpgp*c)-3')	C	DNA	15	Homo sapiens

Sequence of entity 1 (A), FASTA

>7N2M_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

>7N2M_2 RNA (5'-R(*GP*CP*CP*UP*GP*GP*AP*GP*CP*GP*C)-3') (chains B)
GCCUGGAGCGC

Sequence of entity 3 (C), FASTA

>7N2M_3 DNA (5'-D(*AP*T*AP*GP*TP*CP*GP*CP*TP*CP*CP*AP*GP*GP*C)-3') (chains C)
ATAGTCGCTCCAGGC

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	4

Water and common crystallization additives (K, 1PE, SO4) are not listed.

Primary citation

Structural and functional insight into mismatch extension by human DNA polymerase alpha. Baranovskiy, A.G., Babayeva, N.D., Lisova, A.E. et al. Proc Natl Acad Sci U S A (2022) 119:e2111744119-e2111744119. DOI 10.1073/pnas.2111744119 · 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…
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

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