9C8V: Human DNA polymerase alpha/primase - CHAPSO

Human DNA polymerase alpha/primase - CHAPSO (4 mM). Determined by electron microscopy at 3.39 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.39 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,829
Mol. weight: 277.62 kDa
Ligands: ZN, SF4
Released: 4 Sept 2024

Explore 9C8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C8V contains 117 α-helices and 95 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: 26 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-19	11
α-helix	23-31	9
α-helix	32-34	3
β-strand	43-48	6	1
α-helix	50-52	3
β-strand	54-58	5	1
α-helix	63-71	9
β-strand	77-84	8	1
α-helix	88-90	3
β-strand	101-103	3	1
β-strand	106-111	6	2
α-helix	112-114	3
α-helix	129-148	20
β-strand	155-159	5	2
β-strand	164-169	6	2
α-helix	172-175	4
α-helix	179-189	11
α-helix	208-209	2
α-helix	210-223	14
α-helix	224-230	7
α-helix	237-246	10
α-helix	249-251	3
α-helix	252-261	10
α-helix	265-282	18
α-helix	292-301	10
α-helix	307-311	5
β-strand	317-318	2	1
α-helix	319	1
β-strand	323	1	3
β-strand	329	1	4
β-strand	330	1	3
α-helix	332	1
β-strand	333-334	2	2
α-helix	348	1
β-strand	349	1	4
α-helix	350-358	9
α-helix	382-385	4
α-helix	389-410	22

Chain B: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	5
α-helix	39-62	24
α-helix	68-80	13
α-helix	94-110	17
α-helix	114-134	21
α-helix	139-147	9
α-helix	156-161	6
α-helix	163-169	7
β-strand	184-187	4	6
α-helix	189-191	3
α-helix	192-195	4
β-strand	201-203	3	6
β-strand	206-209	4	6
α-helix	211-235	25
α-helix	247-250	4
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-315	13
α-helix	320-332	13
α-helix	338-344	7
α-helix	346-353	8
α-helix	367-372	6
α-helix	391-400	10
α-helix	405-416	12
α-helix	420-431	12
α-helix	444-454	11

Chain C: 55 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	7
β-strand	355-367	13	7
β-strand	372-380	9	7
β-strand	385-391	7	8
β-strand	394-397	4	9
β-strand	402-407	6	9
α-helix	410-416	7
α-helix	417-421	5
β-strand	431-438	8	8
β-strand	449-457	9	8
α-helix	462-465	4
β-strand	473-477	5	8
α-helix	483-490	8
β-strand	498-502	5	7
β-strand	505	1	7
β-strand	512	1	10
β-strand	516-520	5	7
α-helix	523-525	3
β-strand	526-528	3	7
α-helix	533-536	4
β-strand	537-548	12	11
β-strand	555-568	14	11
α-helix	573-575	3
β-strand	581-587	7	11
α-helix	594-595	2
α-helix	598-604	7
β-strand	609-612	4	11
α-helix	615-629	15
β-strand	633-636	4	11
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	10
α-helix	682-685	4
β-strand	689-692	4	11
α-helix	693-700	8
α-helix	708-714	7
α-helix	725-728	4
α-helix	729-733	5
α-helix	735-759	25
α-helix	761-772	12
α-helix	776-781	6
α-helix	784-798	15
β-strand	801	1	8
α-helix	802-807	6
β-strand	844-845	2	12
β-strand	850-852	3	12
β-strand	856-861	6	12
α-helix	864-872	9
α-helix	899-903	5
α-helix	910-929	20
α-helix	936-955	20
α-helix	958-961	4
α-helix	970-993	24
β-strand	998-1002	5	12
β-strand	1005-1009	5	12
α-helix	1015-1032	18
β-strand	1038-1051	14	12
β-strand	1054-1062	9	12
α-helix	1064-1066	3
β-strand	1068-1075	8	12
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	13
α-helix	1143-1145	3
α-helix	1149-1151	3
α-helix	1153-1164	12
α-helix	1167-1169	3
β-strand	1174-1177	4	13
β-strand	1178-1179	2	14
β-strand	1180-1181	2	15
β-strand	1192-1193	2	14
α-helix	1195-1200	6
β-strand	1205-1206	2	15
α-helix	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
α-helix	1232-1239	8
α-helix	1243-1249	7
α-helix	1253-1255	3
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279-1282	4	16
β-strand	1289-1292	4	16
β-strand	1296-1297	2	17
β-strand	1304-1305	2	17
α-helix	1319-1322	4
α-helix	1323-1341	19
β-strand	1346-1348	3	18
β-strand	1356-1357	2	18
β-strand	1364	1	19
β-strand	1369	1	19
β-strand	1370	1	20
α-helix	1371	1
β-strand	1378	1	20
β-strand	1379-1381	3	18
α-helix	1385-1397	13
α-helix	1401-1405	5
α-helix	1411-1420	10
α-helix	1424-1441	18
β-strand	1448-1450	3	5
α-helix	1451-1455	5

Chain D: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-174	5	21
β-strand	193-195	3	22
α-helix	213-235	23
β-strand	247-259	13	23
β-strand	270-274	5	23
β-strand	283-287	5	23
β-strand	295-296	2	24
β-strand	301-308	8	23
β-strand	314-319	6	23
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	25
α-helix	328	1
α-helix	334-336	3
β-strand	340-345	6	21
α-helix	358-370	13
β-strand	374-378	5	21
β-strand	383	1	26
α-helix	387-390	4
α-helix	398-412	15
β-strand	419-423	5	21
β-strand	428	1	26
β-strand	435	1	27
β-strand	437	1	28
α-helix	438-441	4
α-helix	449-451	3
β-strand	453-455	3	21
β-strand	458	1	28
β-strand	460-464	5	22
β-strand	467-471	5	22
α-helix	476-482	7
β-strand	485-486	2	24
α-helix	494-504	11
β-strand	520	1	27
α-helix	522-528	7
β-strand	534	1	25
β-strand	537-539	3	22
β-strand	547-551	5	22
β-strand	554-558	5	22
β-strand	563-564	2	29
β-strand	567-568	2	29
β-strand	570-576	7	21
β-strand	590-597	8	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A	protein	412	Homo sapiens	P49642 (AlphaFold model)
DNA primase large subunit	B	protein	434	Homo sapiens	P49643 (AlphaFold model)
DNA polymerase alpha catalytic subunit	C	protein	1119	Homo sapiens	P09884 (AlphaFold model)
DNA polymerase alpha subunit B	D	protein	444	Homo sapiens	Q14181 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C8V_1 DNA primase small subunit (chains A)
METFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSF
NNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRR
CCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSA
VRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESW
DKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQY
CFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAI
STNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLK

Sequence of entity 2 (B), FASTA

>9C8V_2 DNA primase large subunit (chains B)
YPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESELRKL
KFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQ
DFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGFESIYKIPFADALDLFRGRKVY
LEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAVQSDERLQPLLNHLSHSYTGQD
YSTQGNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLE
QALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDY
HGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSL
NHPNQFFCESQRIL

Sequence of entity 3 (C), FASTA

>9C8V_3 DNA polymerase alpha catalytic subunit (chains C)
EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKID
LNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKY
SAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKAE
AMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKP
PFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISA
KELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMC
ELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLG
DEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFT
TVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPD
LILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLE
VIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAA
LVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLI
EIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSY
VICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIAT
WLGLDPTQFRVHHYHKDEENDALLGGPAQLTDEEKYRDCERFKCPCPTCGTENIYDNVFD
GSGTDMEPSLYRCSNIDCKASPLTFTVQLSNKLIMDIRRFIKKYYDGWLICEEPTCRNRT
RHLPLQFSRTGPLCPACMKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKL
KKQFFTPKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLFA

Sequence of entity 4 (D), FASTA

>9C8V_4 DNA polymerase alpha subunit B (chains D)
ATPSQKYNSRSNRGEVVTSFGLAQGVSWSGRGGAGNISLKVLGCPEALTGSYKSMFQKLP
DIREVLTCKIEELGSELKEHYKIEAFTPLLAPAQEPVTLLGQIGCDSNGKLNNKSVILEG
DREHSSGAQIPVDLSELKEYSLFPGQVVIMEGINTTGRKLVATKLYEGVPLPFYQPTEED
ADFEQSMVLVACGPYTTSDSITYDPLLDLIAVINHDRPDVCILFGPFLDAKHEQVENCLL
TSPFEDIFKQCLRTIIEGTRSSGSHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKKQVQ
FVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFSRILKHILTQRSYYPLYPP
QEDMAIDYESFYVYAQLPVTPDVLIIPSELRYFVKDVLGCVCVNPGRLTKGQVGGTFARL
YLRRPAADGAERQSPCIAVQVVRI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SF4	Iron/sulfur cluster	Fe4 S4	1

Primary citation

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing. Abe, K.M., Li, G., He, Q. et al. Nat Commun (2024) 15:7705-7705. DOI 10.1038/s41467-024-52091-1 · PubMed

Other PDB entries of the same protein (UniProt P49642 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RB4 1.5 Å, Crystal structure of the Pri1 subunit of human primase
4LIK 1.7 Å, Crystal structure of the catalytic subunit of human primase
6R5E 1.85 Å, Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP
6R5D 1.95 Å, Crystal structure of the Pri1 subunit of human primase bound to dATP
4MHQ 2.2 Å, Crystal structure of human primase catalytic subunit
6R4U 2.2 Å, Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate
6R4T 2.35 Å, Crystal structure of the Pri1 subunit of human primase bound to vidarabine triphosphate
4LIL 2.6 Å, Crystal structure of the catalytic subunit of human primase bound to UTP and Mn
4RR2 2.65 Å, Crystal structure of human primase
4BPU 2.7 Å, Crystal structure of human primase in heterodimeric form, comprising PriS and truncated…
6R4S 2.75 Å, Crystal structure of the Pri1 subunit of human primase bound to ATP
8VY3 2.98 Å, Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)

Browse structure collections

About this viewer

MolViewer shows 9C8V 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.