7JK1: DNA-directed primase/polymerase protein

Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion. Determined by X-ray diffraction at 2.62 Å resolution. Released 30 Jun 2021.

Method
X-ray diffraction
Resolution
2.62 Å
Organisms
Homo sapiens, synthetic construct
Chains
6
Atoms
5,429
Mol. weight
101.18 kDa
Ligands
DCP, CA
Released
30 Jun 2021

Explore 7JK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JK1 contains 23 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 A: 14 helices, 17 β-strands

ElementResiduesLengthSheet
α-helix5-139
β-strand43-4531
α-helix48-569
β-strand63-6861
β-strand76-8161
α-helix83-886
β-strand99-10351
β-strand10912
β-strand112-11873
α-helix127-14519
α-helix152-1543
β-strand155-15953
β-strand165-17283
β-strand177-17932
α-helix182-19211
α-helix194-1974
α-helix263-2664
β-strand267-26934
β-strand275-27734
β-strand27913
β-strand288-29141
α-helix2921
β-strand29615
α-helix3021
β-strand30315
α-helix3041
β-strand305-30623
α-helix322-3309
α-helix335-3373
α-helix3411
β-strand342-34432
Chain B: 9 helices, 19 β-strands
ElementResiduesLengthSheet
β-strand43-4536
α-helix48-5811
β-strand63-6866
β-strand76-8166
α-helix83-908
β-strand99-10356
β-strand10912
β-strand112-11877
α-helix127-14519
α-helix152-1543
β-strand155-15957
β-strand165-17287
β-strand177-17932
α-helix182-19211
α-helix194-1974
α-helix263-2664
β-strand267-26938
β-strand275-27738
β-strand279-28027
β-strand288-29146
α-helix2921
β-strand29319
β-strand296110
β-strand303110
β-strand30419
β-strand305-30627
α-helix322-3309
β-strand342-34432

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed primase/polymerase proteinA, Bprotein354Homo sapiensQ96LW4 (AlphaFold model)
DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')C, GDNA17synthetic construct
DNA (5'-d(*gp*gp*tp*gp*tp*gp*gp*tp*ap*gp*cp*g)-3')D, FDNA12synthetic construct
Sequence of entity 1 (A, B), FASTA
>7JK1_1 DNA-directed primase/polymerase protein (chains A, B)
MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKE
DVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKP
ANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFK
DNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATE
ESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGK
RVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Sequence of entity 2 (C, G), FASTA
>7JK1_2 DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3') (chains C, G)
CAGCGCTACCACACCCC
Sequence of entity 3 (D, F), FASTA
>7JK1_3 DNA (5'-D(*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*G)-3') (chains D, F)
GGTGTGGTAGCG

Ligands and cofactors

IDNameFormulaCopies
DCP2'-deoxycytidine-5'-triphosphateC9 H16 N3 O13 P32
CACalcium ionCa2

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Rechkoblit, O., Johnson, R.E., Gupta, Y.K. et al. Nat Commun (2021) 12:4020-4020. DOI 10.1038/s41467-021-24317-z · PubMed

Other PDB entries of the same protein (UniProt Q96LW4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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