5EXR: Human primosome

Crystal structure of human primosome. Determined by X-ray diffraction at 3.6 Å resolution. Released 23 Mar 2016.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 37,658
Mol. weight: 609.23 kDa
Ligands: ZN, SF4
Released: 23 Mar 2016

Explore 5EXR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EXR contains 228 α-helices and 203 β-strands across 8 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: 28 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	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	129-131	3
α-helix	133-148	16
β-strand	155-159	5	2
β-strand	164-169	6	2
α-helix	172-175	4
α-helix	179-188	10
α-helix	210-218	9
α-helix	223-225	3
α-helix	226-230	5
α-helix	237-244	8
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
β-strand	323	1	3
β-strand	329	1	4
β-strand	330	1	3
α-helix	332	1
β-strand	333	1	2
α-helix	334	1
α-helix	336-338	3
α-helix	348	1
β-strand	349	1	4
α-helix	350-355	6
α-helix	389-405	17
α-helix	406-410	5
α-helix	411	1

Chain B: 26 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	94-108	15
α-helix	109-111	3
α-helix	114-123	10
α-helix	125-133	9
α-helix	139-146	8
β-strand	152-153	2	6
α-helix	156-161	6
α-helix	163-169	7
β-strand	184-187	4	6
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-202	2	6
β-strand	206-209	4	6
α-helix	211-234	24
α-helix	247-250	4
α-helix	276-282	7
α-helix	286-297	12
α-helix	303-315	13
α-helix	320-331	12
α-helix	338-341	4
α-helix	342-346	5
α-helix	347-353	7
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-415	11
α-helix	420-432	13
α-helix	444-453	10

Chain C: 48 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	7
β-strand	355-367	13	7
α-helix	368-370	3
β-strand	372-381	10	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
α-helix	423-425	3
β-strand	431-438	8	8
β-strand	449-457	9	8
β-strand	473-477	5	8
α-helix	483-490	8
β-strand	498-502	5	7
β-strand	505	1	7
β-strand	517-520	4	7
α-helix	523-525	3
β-strand	526	1	7
α-helix	533-535	3
β-strand	537-548	12	10
β-strand	555-568	14	10
β-strand	582	1	10
β-strand	585-586	2	10
α-helix	594-595	2
α-helix	598-604	7
β-strand	611	1	10
α-helix	615-629	15
β-strand	633-636	4	10
α-helix	639-643	5
α-helix	644-653	10
α-helix	659-662	4
β-strand	689-692	4	10
α-helix	693-698	6
α-helix	708-714	7
α-helix	729-731	3
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-781	6
α-helix	784-798	15
β-strand	801	1	8
β-strand	850-852	3	11
β-strand	856	1	11
β-strand	859-861	3	12
α-helix	864-871	8
α-helix	907-908	2
α-helix	912-928	17
α-helix	938-958	21
α-helix	970-992	23
β-strand	1000-1002	3	12
β-strand	1005-1007	3	12
β-strand	1009	1	11
α-helix	1015-1032	18
β-strand	1038-1039	2	12
β-strand	1044-1051	8	11
β-strand	1054-1060	7	11
β-strand	1065	1	13
β-strand	1067	1	13
β-strand	1070-1075	6	11
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	14
α-helix	1143-1145	3
α-helix	1149-1151	3
α-helix	1153-1164	12
β-strand	1174-1177	4	14
β-strand	1178-1179	2	15
β-strand	1180-1181	2	16
α-helix	1188-1190	3
β-strand	1192-1193	2	15
α-helix	1195-1199	5
β-strand	1205-1206	2	16
α-helix	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
α-helix	1232-1238	7
α-helix	1243-1249	7
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279-1282	4	17
β-strand	1289-1292	4	17
β-strand	1296-1297	2	18
β-strand	1304-1305	2	18
α-helix	1319-1322	4
α-helix	1323-1343	21
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	1424-1443	20
β-strand	1448-1450	3	5
α-helix	1451-1455	5

Chain D: 15 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-174	5	22
β-strand	193-196	4	23
α-helix	213-234	22
β-strand	251-256	6	24
β-strand	271-274	4	24
α-helix	276-279	4
β-strand	283-287	5	24
β-strand	295-296	2	25
β-strand	301-307	7	24
β-strand	314-319	6	24
α-helix	325-326	2
β-strand	327	1	26
α-helix	328	1
α-helix	333-335	3
α-helix	337-339	3
β-strand	340-346	7	22
α-helix	358-370	13
β-strand	374-378	5	22
β-strand	383	1	27
α-helix	387-390	4
α-helix	398-411	14
β-strand	419-423	5	22
β-strand	428	1	27
β-strand	435	1	28
β-strand	437	1	29
α-helix	438	1
α-helix	449-452	4
β-strand	453-455	3	22
β-strand	458	1	29
β-strand	460-464	5	23
β-strand	468-471	4	23
α-helix	476-480	5
β-strand	485-486	2	25
α-helix	494-505	12
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	590-597	8	22

Chain E: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	23-31	9
α-helix	32-34	3
β-strand	43-48	6	32
α-helix	50-52	3
β-strand	54-58	5	32
α-helix	63-71	9
β-strand	77-84	8	32
α-helix	88-90	3
β-strand	101-103	3	32
β-strand	106-111	6	33
α-helix	112-115	4
α-helix	133-148	16
β-strand	155-159	5	33
β-strand	164-169	6	33
α-helix	172-175	4
α-helix	179-189	11
α-helix	210-226	17
α-helix	237-244	8
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	32
α-helix	319	1
β-strand	323	1	34
β-strand	329	1	35
β-strand	330	1	34
α-helix	332	1
β-strand	333	1	33
α-helix	334	1
α-helix	348	1
β-strand	349	1	35
α-helix	350-355	6
α-helix	389-409	21

Chain F: 26 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	36
α-helix	39-62	24
α-helix	68-80	13
α-helix	94-108	15
α-helix	109-111	3
α-helix	114-123	10
α-helix	126-133	8
α-helix	139-146	8
β-strand	152-153	2	37
α-helix	156-161	6
α-helix	163-169	7
β-strand	184-187	4	37
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-202	2	37
β-strand	206-209	4	37
α-helix	211-235	25
α-helix	247-250	4
α-helix	276-282	7
α-helix	286-297	12
α-helix	303-315	13
α-helix	320-331	12
α-helix	338-341	4
α-helix	342-346	5
α-helix	347-353	7
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-415	11
α-helix	420-432	13
α-helix	444-453	10

Chain G: 47 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	340-351	12	38
β-strand	355-367	13	38
α-helix	368-370	3
β-strand	372-381	10	38
β-strand	385-391	7	39
β-strand	394-397	4	40
β-strand	402-407	6	40
α-helix	410-416	7
α-helix	417-421	5
α-helix	423-425	3
β-strand	431-438	8	39
β-strand	449-457	9	39
β-strand	473-477	5	39
α-helix	483-490	8
β-strand	498-502	5	38
β-strand	505	1	38
β-strand	517-520	4	38
α-helix	523-525	3
β-strand	526	1	38
β-strand	537-548	12	41
β-strand	555-568	14	41
α-helix	573-575	3
β-strand	582	1	41
β-strand	585	1	41
β-strand	586	1	42
α-helix	594-595	2
α-helix	598-604	7
β-strand	611	1	42
α-helix	615-629	15
β-strand	633-636	4	41
α-helix	639-643	5
α-helix	644-653	10
α-helix	659-662	4
β-strand	689-692	4	41
α-helix	693-698	6
α-helix	708-714	7
α-helix	729-731	3
α-helix	735-758	24
α-helix	761-772	12
α-helix	776-781	6
α-helix	784-798	15
β-strand	801	1	39
β-strand	850-852	3	43
β-strand	856	1	43
β-strand	859-861	3	44
α-helix	864-871	8
α-helix	907-908	2
α-helix	910-928	19
α-helix	938-958	21
α-helix	970-992	23
β-strand	1000-1002	3	44
β-strand	1005-1007	3	44
β-strand	1009	1	43
α-helix	1015-1032	18
β-strand	1038-1039	2	44
β-strand	1044-1051	8	43
β-strand	1054-1060	7	43
β-strand	1065	1	45
β-strand	1067	1	45
β-strand	1070-1075	6	43
α-helix	1086-1099	14
α-helix	1105-1125	21
α-helix	1130-1133	4
β-strand	1135-1138	4	46
α-helix	1149-1151	3
α-helix	1153-1164	12
β-strand	1174-1177	4	46
β-strand	1178-1179	2	47
β-strand	1180	1	48
α-helix	1188-1190	3
β-strand	1192-1193	2	47
α-helix	1195-1199	5
β-strand	1206	1	48
α-helix	1208-1210	3
α-helix	1211-1216	6
α-helix	1217-1224	8
α-helix	1232-1238	7
α-helix	1243-1249	7
α-helix	1269-1272	4
α-helix	1277-1278	2
β-strand	1279-1282	4	49
β-strand	1289-1292	4	49
β-strand	1296-1297	2	50
β-strand	1304-1305	2	50
α-helix	1319-1322	4
α-helix	1323-1343	21
β-strand	1346-1348	3	51
β-strand	1356-1357	2	51
β-strand	1364	1	52
β-strand	1369	1	52
β-strand	1370	1	53
β-strand	1378	1	53
β-strand	1379-1381	3	51
α-helix	1385-1398	14
α-helix	1401-1405	5
α-helix	1411-1420	10
α-helix	1424-1443	20
β-strand	1448-1450	3	36
α-helix	1451-1455	5

Chain H: 16 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4
β-strand	170-174	5	54
β-strand	193-196	4	55
α-helix	213-234	22
β-strand	251-256	6	56
β-strand	271-274	4	56
α-helix	276-279	4
β-strand	283-287	5	56
β-strand	295-296	2	57
β-strand	301-307	7	56
β-strand	314-319	6	56
α-helix	325-326	2
β-strand	327	1	58
α-helix	328	1
α-helix	333-335	3
α-helix	337-339	3
β-strand	340-346	7	54
α-helix	358-370	13
β-strand	374-378	5	54
β-strand	383	1	59
α-helix	387-390	4
α-helix	398-412	15
β-strand	419-423	5	54
β-strand	428	1	59
β-strand	435	1	60
β-strand	437	1	61
α-helix	438	1
α-helix	449-452	4
β-strand	453-455	3	54
β-strand	458	1	61
β-strand	460-464	5	55
β-strand	468-471	4	55
α-helix	476-480	5
α-helix	481-483	3
β-strand	485-486	2	57
α-helix	494-505	12
β-strand	507	1	62
β-strand	520	1	60
α-helix	522-528	7
β-strand	530	1	62
β-strand	534	1	58
β-strand	537-539	3	55
β-strand	547-551	5	55
β-strand	554-558	5	55
β-strand	563-564	2	63
β-strand	567-568	2	63
β-strand	570-576	7	54
β-strand	590-597	8	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A, E	protein	420	Homo sapiens	P49642 (AlphaFold model)
DNA primase large subunit	B, F	protein	509	Homo sapiens	P49643 (AlphaFold model)
DNA polymerase alpha catalytic subunit	C, G	protein	1128	Homo sapiens	P09884 (AlphaFold model)
DNA polymerase alpha subunit B	D, H	protein	597	Homo sapiens	Q14181 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5EXR_1 DNA primase small subunit (chains A, E)
METFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSF
NNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRR
CCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSA
VRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESW
DKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQY
CFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAI
STNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLKKSDLQKDF

Sequence of entity 2 (B, F), FASTA

>5EXR_2 DNA primase large subunit (chains B, F)
MEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLG
VSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWF
IQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGF
ESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAV
QSDERLQPLLNHLSHSYTGQDYSTQGNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHH
LRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRT
DYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHY
QVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNGGKDIKKEPIQPETPQPKPSVQKT
KDASSALASLNSSLEMDMEGLEDYFSEDS

Sequence of entity 3 (C, G), FASTA

>5EXR_3 DNA polymerase alpha catalytic subunit (chains C, G)
ADEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREM
KIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLE
VKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWC
KAEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAA
PKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDII
VGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVE
ISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQ
IMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQ
KLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNI
CFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDL
NPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKM
NLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKK
YAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQK
RLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDT
VSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVL
IATWLGLDPTQFRVHHYHKDEENDALLGGPAQLTDEEKYRDCERFKCPCPTCGTENIYDN
VFDGSGTDMEPSLYRCSNIDCKASPLTFTVQLSNKLIMDIRRFIKKYYDGWLICEEPTCR
NRTRHLPLQFSRTGPLCPACMKATLQPEYSDKSLYTQLCFYRYIFDAECALEKLTTDHEK
DKLKKQFFTPKVLQDYRKLKNTAEQFLSRSGYSEVNLSKLFAGCAVKS

Sequence of entity 4 (D, H), FASTA

>5EXR_4 DNA polymerase alpha subunit B (chains D, H)
SASAQQLAEELQIFGLDCEEALIEKLVELCVQYGQNEEGMVGELIAFCTSTHKVGLTSEI
LNSFEHEFLSKRLSKARHSTCKDSGHAGARDIVSIQELIEVEEEEEILLNSYTTPSKGSQ
KRAISTPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQKYNSRSNRGEVVTSFGLAQGVS
WSGRGGAGNISLKVLGCPEALTGSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIEAFT
PLLAPAQEPVTLLGQIGCDSNGKLNNKSVILEGDREHSSGAQIPVDLSELKEYSLFPGQV
VIMEGINTTGRKLVATKLYEGVPLPFYQPTEEDADFEQSMVLVACGPYTTSDSITYDPLL
DLIAVINHDRPDVCILFGPFLDAKHEQVENCLLTSPFEDIFKQCLRTIIEGTRSSGSHLV
FVPSLRDVHHEPVYPQPPFSYSDLSREDKKQVQFVSEPCSLSINGVIFGLTSTDLLFHLG
AEEISSSSGTSDRFSRILKHILTQRSYYPLYPPQEDMAIDYESFYVYAQLPVTPDVLIIP
SELRYFVKDVLGCVCVNPGRLTKGQVGGTFARLYLRRPAADGAERQSPCIAVQVVRI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. Baranovskiy, A.G., Babayeva, N.D., Zhang, Y. et al. J Biol Chem (2016) 291:10006-10020. DOI 10.1074/jbc.M116.717405 · 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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MolViewer shows 5EXR 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.