4FYD: Yeast DNA polymerase alpha

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP. Determined by X-ray diffraction at 3.1 Å resolution. Released 27 Feb 2013.

Method
X-ray diffraction
Resolution
3.1 Å
Organism
Saccharomyces cerevisiae
Chains
6
Atoms
14,744
Mol. weight
230.93 kDa
Ligands
DGT
Released
27 Feb 2013

Explore 4FYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FYD contains 80 α-helices and 66 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 A: 40 helices, 34 β-strands

ElementResiduesLengthSheet
β-strand352-362111
β-strand365-37391
β-strand379-38681
β-strand390-39782
α-helix403-41816
β-strand425-43172
β-strand442-451102
α-helix461-4633
β-strand471-47552
α-helix481-4888
β-strand496-49941
β-strand50311
β-strand515-51951
α-helix522-5243
β-strand525-52731
α-helix534-5352
β-strand536-548133
β-strand553-567153
α-helix572-5743
β-strand581-58663
α-helix598-6058
β-strand609-61243
α-helix616-63015
β-strand634-63743
α-helix640-6445
α-helix645-65410
α-helix660-6634
α-helix683-6908
β-strand695-69843
α-helix702-7076
α-helix716-7249
α-helix739-7424
α-helix744-76724
α-helix770-78112
α-helix785-7906
α-helix794-80613
β-strand81012
α-helix811-8144
β-strand84814
α-helix849-8513
β-strand854-85635
β-strand860-86565
α-helix868-8758
β-strand88416
β-strand89516
α-helix902-9032
α-helix905-92521
α-helix930-95223
α-helix964-98623
β-strand991-99555
β-strand99614
β-strand999-100355
α-helix1009-102416
β-strand1032-1045145
β-strand1048-105695
β-strand1062-106985
α-helix1072-10743
α-helix1080-109314
α-helix1099-111921
α-helix1124-11274
β-strand1129-113247
α-helix1141-11444
α-helix1147-115812
β-strand1167-117267
β-strand117318
α-helix1190-11923
β-strand1193-119537
α-helix1196-11994
α-helix1202-12043
β-strand120818
α-helix1210-12123
α-helix1213-12197
α-helix1220-12267
α-helix1234-12418
Chain B: 40 helices, 32 β-strands
ElementResiduesLengthSheet
β-strand352-362119
β-strand365-37399
β-strand379-38689
β-strand390-397810
α-helix403-41816
β-strand425-431710
β-strand442-4511010
α-helix461-4633
β-strand471-475510
α-helix481-4888
β-strand496-49949
β-strand50319
β-strand515-51959
α-helix522-5243
β-strand525-52739
α-helix534-5352
β-strand536-5481311
β-strand553-5671511
α-helix572-5743
β-strand581-586611
α-helix598-6058
β-strand609-612411
α-helix616-63015
β-strand634-637411
α-helix640-6445
α-helix645-65410
α-helix660-6634
α-helix683-6908
β-strand695-698411
α-helix702-7076
α-helix716-7249
α-helix739-7424
α-helix744-76724
α-helix770-78112
α-helix785-7906
α-helix794-80613
β-strand810110
α-helix811-8144
β-strand848112
α-helix849-8513
β-strand854-856313
β-strand860-865613
α-helix868-8758
α-helix902-9032
α-helix905-92521
α-helix930-95223
α-helix964-98623
β-strand991-995513
β-strand996112
β-strand999-1003513
α-helix1009-102416
β-strand1032-10451413
β-strand1048-1056913
β-strand1062-1069813
α-helix1072-10743
α-helix1080-109314
α-helix1099-111921
α-helix1124-11274
β-strand1129-1132414
α-helix1141-11444
α-helix1147-115812
β-strand1167-1172614
β-strand1173115
α-helix1190-11923
β-strand1193-1195314
α-helix1196-11994
α-helix1202-12043
β-strand1208115
α-helix1210-12123
α-helix1213-12197
α-helix1220-12267
α-helix1234-12418

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA polymerase alpha catalytic subunit AA, Bprotein910Saccharomyces cerevisiaeP13382 (AlphaFold model)
DNA (5'-d(*tp*gp*ap*gp*cp*gp*tp*g*tp*gp*tp*ap*cp*cp*cp*cp*tp*gp*cp*cp*cp*gp*cp*cp*g)-3')C, DDNA25
Dna/rna (5'-r(*cp*gp*gp*cp*gp*gp*gp*cp*ap*g)-d(p*gp*g)-3')E, FNA-hybrid12
Sequence of entity 1 (A, B), FASTA
>4FYD_1 DNA polymerase alpha catalytic subunit A (chains A, B)
TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHE
EIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSS
DTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIAAASHCAVEVSVDKPQNITPT
TTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRP
PQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVL
AHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLT
PKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRI
QLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQN
EENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKE
DIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTAN
SMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNSVMIDTGCDN
YADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEV
KGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYK
INMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALS
VAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKY
FRREGGNNNG
Sequence of entity 2 (C, D), FASTA
>4FYD_2 DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') (chains C, D)
TGAGCGTGTGTACCCCTGCCCGCCG
Sequence of entity 3 (E, F), FASTA
>4FYD_3 DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') (chains E, F)
CGGCGGGCAGGG

Ligands and cofactors

IDNameFormulaCopies
DGT2'-deoxyguanosine-5'-triphosphateC10 H16 N5 O13 P32

Primary citation

Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha. Perera, R.L., Torella, R., Klinge, S. et al. Elife (2013) 2:e00482. DOI 10.7554/eLife.00482 · PubMed

Other PDB entries of the same protein (UniProt P13382 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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