8D96: DNA primase large subunit

Human DNA polymerase alpha/primase elongation complex I bound to primer/template. Determined by electron microscopy at 3.35 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.35 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,203
Mol. weight: 236.63 kDa
Ligands: SF4, MG, DTP
Released: 19 Apr 2023

Explore 8D96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D96 contains 56 α-helices and 36 β-strands across 2 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 B: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-316	14
α-helix	320-333	14
α-helix	338-344	7
α-helix	346-352	7
α-helix	363-366	4
α-helix	367-372	6
α-helix	391-400	10
α-helix	405-416	12
α-helix	421-431	11
α-helix	444-455	12

Chain C: 44 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	1
β-strand	355-367	13	1
β-strand	372-381	10	1
β-strand	384-391	8	2
α-helix	406-409	4
α-helix	410-416	7
α-helix	417-421	5
α-helix	422-425	4
β-strand	431-438	8	2
β-strand	449-458	10	2
β-strand	473-477	5	2
α-helix	483-491	9
β-strand	498-502	5	1
β-strand	505	1	1
β-strand	512	1	3
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	4
β-strand	555-568	14	4
α-helix	573-575	3
β-strand	581-587	7	4
α-helix	594-595	2
α-helix	598-605	8
β-strand	609-612	4	4
α-helix	615-629	15
β-strand	633-636	4	4
α-helix	639-643	5
α-helix	644-654	11
α-helix	659-662	4
β-strand	665	1	3
α-helix	680-684	5
β-strand	689-692	4	4
α-helix	693-700	8
α-helix	708-711	4
α-helix	712-716	5
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	2
α-helix	803-807	5
β-strand	844	1	5
α-helix	845-847	3
β-strand	850-852	3	6
β-strand	856-861	6	6
α-helix	864-872	9
α-helix	898-903	6
α-helix	907-908	2
α-helix	910-930	21
α-helix	936-959	24
α-helix	970-992	23
β-strand	997-1000	4	6
β-strand	1002	1	5
β-strand	1006-1009	4	6
α-helix	1015-1032	18
β-strand	1038-1040	3	6
β-strand	1044-1051	8	6
β-strand	1054-1064	11	6
β-strand	1067-1075	9	6
α-helix	1078-1080	3
α-helix	1086-1100	15
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	7
α-helix	1143-1145	3
α-helix	1153-1164	12
β-strand	1174-1177	4	7
β-strand	1178-1179	2	8
β-strand	1180-1181	2	9
α-helix	1188-1190	3
β-strand	1192-1193	2	8
α-helix	1195-1200	6
β-strand	1205-1206	2	9
α-helix	1208-1214	7
α-helix	1216-1223	8
α-helix	1232-1239	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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/rna (5'-GTP)-r(pgpcpgpgpcpapcpg)-d(papcp*c)-3')	E	NA-hybrid	12	Homo sapiens
DNA (5'-d(aptpapaptpgpgptpcpgptpgpcpcpgpcpcpapaptpapa)-3')	F	DNA	22	Homo sapiens

Sequence of entity 1 (B), FASTA

>8D96_1 DNA primase large subunit (chains B)
MEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLG
VSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWF
IQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGF
ESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAV
QSDERLQPLLNHLSHSYTGQDYSTQGNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHH
LRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRT
DYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHY
QVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNGGKDIKKEPIQPETPQPKPSVQKT
KDASSALASLNSSLEMDMEGLEDYFSEDS

Sequence of entity 2 (C), FASTA

>8D96_2 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 3 (E), FASTA

>8D96_3 DNA/RNA (5'-GTP)-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') (chains E)
GGCGGCACGACC

Sequence of entity 4 (F), FASTA

>8D96_4 DNA (5'-D(*AP*TP*AP*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') (chains F)
ATAATGGTCGTGCCGCCAATAA

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	1
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 P49643 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3L9Q 1.7 Å, Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain
5I7M 1.93 Å, Crystal structure of Y345F mutant of human primase p58 iron-sulfur cluster domain
6DHW 2.01 Å, Crystal structure of primase iron-sulfur domain (266-457)
5F0Q 2.21 Å, Crystal structure of C-terminal domain of the human DNA primase large subunit with bound…
5DQO 2.3 Å, Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain
3Q36 2.5 Å, Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit
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…
8VY3 2.98 Å, Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)
5F0S 3.0 Å, Crystal structure of C-terminal domain of the human DNA primase large subunit with bound…
4BPW 3.0 Å, Crystal structure of human primase bound to UTP
8QJ7 3.07 Å, Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

Browse structure collections

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