8D9D: DNA primase small subunit

Human DNA polymerase-alpha/primase elongation complex II bound to primer/template. Determined by electron microscopy at 3.59 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.59 Å
Organism: Homo sapiens
Chains: 6
Atoms: 19,409
Mol. weight: 334.97 kDa
Ligands: ZN, SF4, MG, DTP
Released: 19 Apr 2023

Explore 8D9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D9D contains 125 α-helices and 100 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: 27 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	112-115	4
α-helix	129-144	16
α-helix	145-149	5
β-strand	155-159	5	2
β-strand	164-169	6	2
α-helix	174-176	3
α-helix	179-188	10
α-helix	210-223	14
α-helix	224-231	8
α-helix	237-246	10
α-helix	249-251	3
α-helix	252-260	9
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
β-strand	333	1	2
α-helix	334-335	2
α-helix	336-341	6
α-helix	344-346	3
α-helix	348	1
β-strand	349	1	4
α-helix	350-358	9
α-helix	389-409	21

Chain B: 25 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	5
α-helix	39-62	24
α-helix	68-80	13
α-helix	93-107	15
α-helix	114-133	20
α-helix	140-146	7
β-strand	152-153	2	6
α-helix	156-161	6
α-helix	163-169	7
β-strand	183-187	5	6
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-203	3	6
β-strand	206-210	5	6
α-helix	214-235	22
α-helix	238-241	4
α-helix	247-251	5
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-316	14
α-helix	320-332	13
α-helix	338-344	7
α-helix	346-353	8
α-helix	363-366	4
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-399	9
α-helix	405-416	12
α-helix	420-432	13
α-helix	444-455	12

Chain C: 58 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	7
β-strand	355-367	13	7
β-strand	372-380	9	7
α-helix	383-384	2
β-strand	385-391	7	8
α-helix	406-409	4
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-424	3
β-strand	431-438	8	8
β-strand	449-457	9	8
β-strand	473-477	5	8
α-helix	483-491	9
β-strand	498-502	5	7
β-strand	505	1	7
β-strand	512	1	9
β-strand	516-520	5	7
α-helix	523-525	3
β-strand	526-529	4	7
α-helix	533-536	4
β-strand	537-548	12	10
β-strand	555-568	14	10
α-helix	573-575	3
β-strand	581-586	6	10
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-611	3	10
α-helix	615-629	15
β-strand	633-636	4	10
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	9
α-helix	679-684	6
β-strand	689-692	4	10
α-helix	693-700	8
α-helix	708-715	8
α-helix	726-728	3
α-helix	730-732	3
α-helix	735-759	25
α-helix	761-772	12
α-helix	776-779	4
α-helix	785-798	14
β-strand	801	1	8
α-helix	803-807	5
β-strand	844	1	11
α-helix	845-847	3
β-strand	850-852	3	12
β-strand	856-861	6	12
α-helix	864-872	9
α-helix	898-903	6
α-helix	907-908	2
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	12
β-strand	1002	1	11
β-strand	1005-1009	5	12
α-helix	1015-1032	18
β-strand	1038-1051	14	12
β-strand	1054-1064	11	12
β-strand	1067-1075	9	12
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	13
α-helix	1143-1145	3
α-helix	1149-1151	3
α-helix	1153-1163	11
β-strand	1174-1177	4	13
β-strand	1178-1179	2	14
β-strand	1180-1181	2	15
α-helix	1188-1190	3
β-strand	1192-1193	2	14
α-helix	1195-1197	3
β-strand	1205-1206	2	15
α-helix	1208-1210	3
α-helix	1211-1215	5
α-helix	1216-1223	8
α-helix	1232-1239	8
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279	1	16
β-strand	1282	1	17
α-helix	1288	1
β-strand	1289	1	17
α-helix	1290	1
β-strand	1292	1	16
β-strand	1296-1297	2	18
α-helix	1300-1302	3
β-strand	1304-1305	2	18
α-helix	1323-1342	20
β-strand	1346-1348	3	19
β-strand	1356-1357	2	19
β-strand	1364	1	20
β-strand	1369	1	20
β-strand	1370	1	21
β-strand	1378	1	21
β-strand	1379-1381	3	19
α-helix	1385-1398	14
α-helix	1401-1405	5
α-helix	1411-1420	10
α-helix	1424-1442	19
β-strand	1448-1450	3	5
α-helix	1451-1455	5

Chain D: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	159-163	5
β-strand	170-174	5	22
β-strand	193-195	3	23
α-helix	213-235	23
β-strand	241	1	24
β-strand	247-259	13	24
α-helix	267-269	3
β-strand	270-274	5	24
β-strand	283-287	5	24
β-strand	295-296	2	25
β-strand	301-308	8	24
β-strand	314-319	6	24
α-helix	320-322	3
α-helix	324-326	3
β-strand	327	1	26
α-helix	328	1
α-helix	334-336	3
β-strand	340-345	6	22
α-helix	358-370	13
β-strand	374-378	5	22
β-strand	383	1	27
α-helix	387-390	4
α-helix	398-412	15
β-strand	419-423	5	22
β-strand	428	1	27
β-strand	435	1	28
β-strand	437	1	29
α-helix	438-440	3
α-helix	447-450	4
β-strand	453-455	3	22
β-strand	458	1	29
β-strand	460-464	5	23
β-strand	467-471	5	23
α-helix	476-481	6
β-strand	485-486	2	25
α-helix	494-504	11
β-strand	507	1	30
β-strand	520	1	28
α-helix	522-528	7
β-strand	530	1	30
β-strand	534	1	26
β-strand	537-539	3	23
β-strand	547-551	5	23
β-strand	554-558	5	23
β-strand	563-564	2	31
β-strand	567-568	2	31
β-strand	570-576	7	22
β-strand	593-597	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A	protein	420	Homo sapiens	P49642 (AlphaFold model)
DNA primase large subunit	B	protein	509	Homo sapiens	P49643 (AlphaFold model)
DNA polymerase alpha catalytic subunit	C	protein	1462	Homo sapiens	P09884 (AlphaFold model)
DNA polymerase alpha subunit B	D	protein	444	Homo sapiens	Q14181 (AlphaFold model)
Dna/rna (5'-d((gtp))-r(pgpcpgpgpcpapcpg)-d(papcpc)-3')	E	NA-hybrid	12	Homo sapiens
DNA (5'-d(aptpgpgptpcpgptpgpcpcpgpcpcpapaptpap*a)-3')	F	DNA	19	Homo sapiens

Sequence of entity 1 (A), FASTA

>8D9D_1 DNA primase small subunit (chains A)
METFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSF
NNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRR
CCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSA
VRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESW
DKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQY
CFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAI
STNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLKKSDLQKDF

Sequence of entity 2 (B), FASTA

>8D9D_2 DNA primase large subunit (chains B)
MEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLG
VSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWF
IQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGF
ESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAV
QSDERLQPLLNHLSHSYTGQDYSTQGNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHH
LRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRT
DYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHY
QVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNGGKDIKKEPIQPETPQPKPSVQKT
KDASSALASLNSSLEMDMEGLEDYFSEDS

Sequence of entity 3 (C), FASTA

>8D9D_3 DNA polymerase alpha catalytic subunit (chains C)
MAPVHGDDSLSDSGSFVSSRARREKKSKKGRQEALERLKKAKAGEKYKYEVEDFTGVYEE
VDEEQYSKLVQARQDDDWIVDDDGIGYVEDGREIFDDDLEDDALDADEKGKDGKARNKDK
RNVKKLAVTKPNNIKSMFIACAGKKTADKAVDLSKDGLLGDILQDLNTETPQITPPPVMI
LKKKRSIGASPNPFSVHTATAVPSGKIASPVSRKEPPLTPVPLKRAEFAGDDVQVESTEE
EQESGAMEFEDGDFDEPMEVEEVDLEPMAAKAWDKESEPAEEVKQEADSGKGTVSYLGSF
LPDVSCWDIDQEGDSSFSVQEVQVDSSHLPLVKGADEEQVFHFYWLDAYEDQYNQPGVVF
LFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEK
IATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTN
TSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKVEAMALKPDLVNVIKDVSPPPLVVM
AFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDCIFPYAFKE
VIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWS
KIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTER
VVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTL
MGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYA
GGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPE
LPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCL
GFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFK
LGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIV
RRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALT
KDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQK
QDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIATWLGLDPTQFRVHHYHKDEENDAL
LGGPAQLTDEEKYRDCERFKCPCPTCGTENIYDNVFDGSGTDMEPSLYRCSNIDCKASPL
TFTVQLSNKLIMDIRRFIKKYYDGWLICEEPTCRNRTRHLPLQFSRTGPLCPACMKATLQ
PEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEKDKLKKQFFTPKVLQDYRKLKNTAEQF
LSRSGYSEVNLSKLFAGCAVKS

Sequence of entity 4 (D), FASTA

>8D9D_4 DNA polymerase alpha subunit B (chains D)
ATPSQKYNSRSNRGEVVTSFGLAQGVSWSGRGGAGNISLKVLGCPEALTGSYKSMFQKLP
DIREVLTCKIEELGSELKEHYKIEAFTPLLAPAQEPVTLLGQIGCDSNGKLNNKSVILEG
DREHSSGAQIPVDLSELKEYSLFPGQVVIMEGINTTGRKLVATKLYEGVPLPFYQPTEED
ADFEQSMVLVACGPYTTSDSITYDPLLDLIAVINHDRPDVCILFGPFLDAKHEQVENCLL
TSPFEDIFKQCLRTIIEGTRSSGSHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKKQVQ
FVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFSRILKHILTQRSYYPLYPP
QEDMAIDYESFYVYAQLPVTPDVLIIPSELRYFVKDVLGCVCVNPGRLTKGQVGGTFARL
YLRRPAADGAERQSPCIAVQVVRI

Sequence of entity 5 (E), FASTA

>8D9D_5 DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') (chains E)
GGCGGCACGACC

Sequence of entity 6 (F), FASTA

>8D9D_6 DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') (chains F)
ATGGTCGTGCCGCCAATAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	2
DTP	2'-deoxyadenosine 5'-triphosphate	C10 H16 N5 O12 P3	1

Primary citation

Structures of human primosome elongation complexes. He, Q., Baranovskiy, A.G., Morstadt, L.M. et al. Nat Struct Mol Biol (2023) 30:579-583. DOI 10.1038/s41594-023-00971-3 · 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)

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