7JKP: DNA-directed primase/polymerase protein

Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion. Determined by X-ray diffraction at 2.59 Å resolution. Released 30 Jun 2021.

Method
X-ray diffraction
Resolution
2.59 Å
Organisms
Homo sapiens, synthetic construct
Chains
6
Atoms
5,291
Mol. weight
101.64 kDa
Ligands
DTP, CA
Released
30 Jun 2021

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

Secondary structure: helices and β-sheets

7JKP contains 23 α-helices and 33 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: 12 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix2-1312
β-strand43-4531
α-helix48-569
β-strand63-6861
β-strand76-8161
α-helix83-886
β-strand99-10351
β-strand10912
β-strand112-11873
α-helix127-14620
α-helix152-1543
β-strand155-15953
β-strand16213
β-strand165-17283
β-strand177-17932
α-helix182-19211
α-helix194-1985
α-helix264-2663
β-strand267-26934
β-strand275-27734
β-strand27913
β-strand288-29141
α-helix2921
β-strand305-30623
α-helix314-3163
α-helix322-3309
α-helix335-3373
β-strand342-34432
Chain B: 11 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand43-4535
α-helix48-5811
β-strand63-6865
β-strand76-8165
α-helix83-908
β-strand99-10355
β-strand10912
β-strand112-11546
α-helix127-14620
α-helix152-1543
β-strand155-15956
β-strand168-17256
β-strand177-17932
α-helix182-19211
α-helix194-1996
α-helix264-2663
β-strand26717
β-strand27717
β-strand27916
β-strand288-29145
α-helix2921
β-strand305-30626
α-helix314-3163
β-strand31718
β-strand32018
α-helix322-3309
α-helix335-3373
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*gp*tp*gp*tp*gp*gp*tp*ap*gp*cp*g)-3')D, HDNA13synthetic construct
Sequence of entity 1 (A, B), FASTA
>7JKP_1 DNA-directed primase/polymerase protein (chains A, B)
MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKE
DVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKP
ANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFK
DNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATE
ESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGK
RVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Sequence of entity 2 (C, G), FASTA
>7JKP_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, H), FASTA
>7JKP_3 DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*G)-3') (chains D, H)
GGGTGTGGTAGCG

Ligands and cofactors

IDNameFormulaCopies
DTP2'-deoxyadenosine 5'-triphosphateC10 H16 N5 O12 P32
CACalcium ionCa3

Water and common crystallization additives (GOL) 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

About this viewer

MolViewer shows 7JKP 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.