8FOC: DNA primase large subunit

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase in Apo state conformation I. Determined by electron microscopy at 3.7 Å resolution. Released 31 May 2023.

Method
Electron microscopy
Resolution
3.7 Å
Organism
Saccharomyces cerevisiae
Chains
4
Atoms
18,382
Mol. weight
356.35 kDa
Ligands
SF4
Released
31 May 2023

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

Secondary structure: helices and β-sheets

8FOC contains 130 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 1: 49 helices, 43 β-strands

ElementResiduesLengthSheet
β-strand352-3621117
β-strand365-373917
β-strand379-386817
β-strand390-397818
α-helix3981
α-helix403-41816
β-strand425-431718
β-strand442-4511018
β-strand471-475518
α-helix481-4888
β-strand496-499417
β-strand503117
β-strand511119
β-strand515-519517
α-helix522-5243
β-strand525-527317
α-helix534-5352
β-strand536-5481320
β-strand553-5671520
α-helix572-5743
β-strand581-586620
α-helix594-5952
α-helix598-6058
β-strand609-612420
α-helix616-63015
β-strand634-637420
α-helix640-6445
α-helix645-65410
α-helix660-6634
β-strand666119
α-helix682-6909
β-strand695-698420
α-helix702-7076
α-helix716-7249
α-helix738-7414
α-helix744-76724
α-helix770-78112
α-helix785-7906
α-helix793-80715
β-strand810118
α-helix811-8144
β-strand849121
β-strand854-856321
β-strand860-864521
α-helix868-8758
α-helix896-8983
α-helix902-9032
α-helix905-92622
α-helix930-94920
α-helix952-9554
α-helix964-98724
β-strand991-995521
β-strand999-1003521
α-helix1009-102618
β-strand1033-10451321
β-strand1048-1054721
β-strand1064-1069621
α-helix1080-109314
α-helix1101-111919
α-helix1124-11274
β-strand1129-1132422
α-helix1137-11393
α-helix1147-115812
α-helix11661
β-strand1167-1172622
β-strand1173123
β-strand1193-1195322
α-helix1196-12005
α-helix1202-12043
β-strand1208123
α-helix1210-12123
α-helix1213-12197
α-helix1220-12256
β-strand1283-1286424
β-strand1293-1296424
β-strand1305-1308425
β-strand1311-1314425
α-helix13191
β-strand1320125
α-helix1321-13222
α-helix1323-134220
β-strand1346-1348326
β-strand1356-1357226
β-strand1366127
α-helix13741
β-strand1375127
β-strand1376-1378326
α-helix1382-139514
α-helix1398-14036
α-helix1406-14083
α-helix1424-143310
α-helix1435-144915
Chain A: 30 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix8-114
α-helix12-2110
α-helix25-339
α-helix40-434
β-strand45-5062
β-strand56-6052
α-helix65-7511
β-strand79-8682
α-helix90-956
β-strand103-10532
β-strand108-11253
α-helix114-1207
α-helix134-14613
α-helix147-1515
β-strand157-16153
β-strand167-17153
α-helix174-1774
α-helix181-19111
α-helix209-2102
α-helix211-22414
α-helix225-2328
α-helix234-2363
α-helix238-2403
α-helix241-2455
α-helix246-2483
α-helix252-26413
α-helix270-28415
α-helix290-30920
β-strand313-31423
α-helix315-3195
β-strand325-32622
α-helix3271
α-helix3301
β-strand33114
α-helix3321
β-strand33715
β-strand33814
β-strand341-34223
α-helix348-3503
α-helix3521
β-strand35315
α-helix354-36310
α-helix367-3693
α-helix373-40129
Chain B: 28 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix44-5411
α-helix72-9423
α-helix99-11214
α-helix121-13818
α-helix142-16221
α-helix165-1739
β-strand181-18221
α-helix183-1842
α-helix185-1906
α-helix192-20716
α-helix212-22110
β-strand225-22841
α-helix229-2324
α-helix233-2375
β-strand242-24431
β-strand247-24931
α-helix255-28127
α-helix288-29710
α-helix323-3253
α-helix327-3304
α-helix335-34713
α-helix352-36413
α-helix369-38113
α-helix388-3947
α-helix396-4027
α-helix412-4154
α-helix417-4215
α-helix435-4384
α-helix441-45010
α-helix455-46612
α-helix470-48213
α-helix500-52526
Chain C: 23 helices, 34 β-strands
ElementResiduesLengthSheet
α-helix254-27623
α-helix280-2823
β-strand28316
β-strand294-30296
β-strand316-31946
α-helix322-3254
β-strand329-33356
β-strand340-34237
β-strand347-35376
β-strand360-36566
α-helix367-3748
β-strand375-37738
α-helix378-38811
α-helix3921
β-strand393-39979
α-helix411-4199
α-helix420-4245
β-strand428-43259
β-strand437110
α-helix441-4444
α-helix461-4688
α-helix470-4745
β-strand481-48559
β-strand490110
β-strand498111
β-strand500112
α-helix501-5033
β-strand515-51739
β-strand520112
β-strand522-526513
β-strand529-533513
α-helix538-5414
β-strand545-54737
α-helix549-5535
α-helix556-56712
β-strand569114
α-helix576-5772
β-strand578-579215
β-strand608-609215
β-strand612111
α-helix614-6207
β-strand621114
α-helix6221
α-helix623-6253
α-helix626-6283
β-strand630-632313
β-strand640-644513
β-strand647-651513
β-strand656116
β-strand662116
β-strand665-67069
α-helix671-6733
β-strand681-68338
α-helix6841
β-strand689-69138
α-helix694-6974
β-strand698-70369

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA primase large subunitBprotein528Saccharomyces cerevisiaeP20457 (AlphaFold model)
DNA primaseAprotein409Saccharomyces cerevisiaeP10363 (AlphaFold model)
DNA polymerase alpha subunit BCprotein705Saccharomyces cerevisiaeP38121 (AlphaFold model)
DNA polymerase1protein1468Saccharomyces cerevisiaeP13382 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>8FOC_1 DNA primase large subunit (chains B)
MFRQSKRRIASRKNFSSYDDIVKSELDVGNTNAANQIILSSSSSEEEKKLYARLYESKLS
FYDLPPQGEITLEQFEIWAIDRLKILLEIESCLSRNKSIKEIETIIKPQFQKLLPFNTES
LEDRKKDYYSHFILRLCFCRSKELREKFVRAETFLFKIRFNMLTSTDQTKFVQSLDLPLL
QFISNEEKAELSHQLYQTVSASLQFQLNLNEEHQRKQYFQQEKFIKLPFENVIELVGNRL
VFLKDGYAYLPQFQQLNLLSNEFASKLNQELIKTYQYLPRLNEDDRLLPILNHLSSGYTI
ADFNQQKANQFSENVDDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSL
FLKGIGLSADEALKFWSEAFTRNGNMTMEKFNKEYRYSFRHNYGLEGNRINYKPWDCHTI
LSKPRPGRGDYHGCPFRDWSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEM
THNSASADLEIGEQTHIAHPNLYFERSRQLQKKQQKLEKEKLFNNGNH
Sequence of entity 2 (A), FASTA
>8FOC_2 DNA primase (chains A)
MTNSVKTNGPSSSDMEYYYKSLYPFKHIFNWLNHSPKPSRDMINREFAMAFRSGAYKRYN
SFNSVQDFKAQIEKANPDRFEIGAIYNKPPRERDTLLKSELKALEKELVFDIDMDDYDAF
RTCCSGAQVCSKCWKFISLAMKITNTALREDFGYKDFIWVFSGRRGAHCWVSDKRARALT
DVQRRNVLDYVNVIRDRNTDKRLALKRPYHPHLARSLEQLKPFFVSIMLEEQNPWEDDQH
AIQTLLPALYDKQLIDSLKKYWLDNPRRSSKEKWNDIDQIATSLFKGPKQDSHIIKLREC
KEDLVLMTLYPKLDVEVTKQTIHLLKAPFCIHPATGNVCVPIDESFAPEKAPKLIDLQTE
MEKNNDVSLTALQPFINQFQAYVSSLLKNELGSVKREREDDDEPASLDF
Sequence of entity 3 (C), FASTA
>8FOC_3 DNA polymerase alpha subunit B (chains C)
MSGSIDVITHFGPDADKPEIITALENLTKLHALSVEDLYIKWEQFSNQRRQTHTDLTSKN
IDEFKQFLQLQMEKRANQISSSSKVNTSTKKPVIKKSLNSSPLFGLSIPKTPTLKKRKLH
GPFSLSDSKQTYNVGSEAETNEKGNSSLKLEFTPGMAEDAVGDSAPLSHAKSSDAKTPGS
STFQTPTTNTPTTSRQNVPAGEILDSLNPENIEISSGNPNVGLLSTEEPSYNQVKVEPFY
DAKKYKFRTMRQNLQEASDVLDDQIESFTKIIQNHYKLSPNDFADPTIQSQSEIYAVGRI
VPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAFKGKNANGDYF
TVNSILPLPYPNSPVSTSQELQEFQANLEGSSLKVIVTCGPYFANDNFSLELLQEFIDSI
NNEVKPHVLIMFGPFIDITHPLIASGKLPNFPQFKTQPKTLDELFLKLFTPILKTISPHI
QTVLIPSTKDAISNHAAYPQASLIRKALQLPKRNFKCMANPSSFQINEIYFGCSNVDTFK
DLKEVIKGGTTSSRYRLDRVSEHILQQRRYYPIFPGSIRTRIKPKDVSTKKETNDMESKE
EKVYEHISGADLDVSYLGLTEFVGGFSPDIMIIPSELQHFARVVQNVVVINPGRFIRATG
NRGSYAQITVQCPDLEDGKLTLVEGEEPVYLHNVWKRARVDLIAS
Sequence of entity 4 (1), FASTA
>8FOC_4 DNA polymerase (chains 1)
MSSKSEKLEKLRKLQAARNGTSIDDYEGDESDGDRIYDEIDEKEYRARKRQELLHDDFVV
DDDGVGYVDRGVEEDWREVDNSSSDEDTGNLASKDSKRKKNIKREKDHQITDMLRTQHSK
STLLAHAKKSQKKSIPIDNFDDILGEFESGEVEKPNILLPSKLRENLNSSPTSEFKSSIK
RVNGNDESSHDAGISKKVKIDPDSSTDKYLEIESSPLKLQSRKLRYANDVQDLLDDVENS
PVVATKRQNVLQDTLLANPPSAQSLADEEDDEDSDEDIILKRRTMRSVTTTRRVNIDSRS
NPSTSPFVTAPGTPIGIKGLTPSKSLQSNTDVATLAVNVKKEDVVDPETDTFQMFWLDYC
EVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGL
DNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSN
IFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLS
LSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAA
LAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTF
SSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMY
QVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNL
AGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKK
AKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSE
VDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSR
FYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFK
RLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCP
LSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAY
PGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVM
IKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKYFRREGGNNNGED
INNLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQL
FTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGCTGVMRYKY
SDKQLYNQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMET
GRSVVQKYLNDCGRRYVDMTSIFDFMLN

Ligands and cofactors

IDNameFormulaCopies
SF4Iron/sulfur clusterFe4 S41

Primary citation

Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase. Yuan, Z., Georgescu, R., Li, H. et al. Nat Commun (2023) 14:3697-3697. DOI 10.1038/s41467-023-39441-1 · PubMed

Other PDB entries of the same protein (UniProt P20457 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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