7JKL: DNA-directed primase/polymerase protein

Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated). Determined by X-ray diffraction at 2.38 Å resolution. Released 30 Jun 2021.

Method
X-ray diffraction
Resolution
2.38 Å
Organisms
Homo sapiens, synthetic construct
Chains
6
Atoms
5,482
Mol. weight
101.7 kDa
Ligands
DTP, CA
Released
30 Jun 2021

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

Secondary structure: helices and β-sheets

7JKL contains 25 α-helices and 34 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, 15 β-strands

ElementResiduesLengthSheet
α-helix2-1413
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-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
α-helix302-3043
β-strand305-30623
α-helix314-3163
α-helix322-3309
α-helix335-3373
α-helix3411
β-strand342-34432
Chain B: 11 helices, 19 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
β-strand11817
α-helix127-14620
α-helix152-1543
β-strand155-15956
β-strand16517
β-strand168-17256
β-strand177-17932
α-helix182-19211
α-helix194-1985
α-helix264-2663
β-strand267-26938
β-strand275-27738
β-strand27916
β-strand288-29145
α-helix2921
β-strand305-30626
α-helix314-3163
β-strand31719
β-strand32019
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*(ddg))-3')D, HDNA13synthetic construct
Sequence of entity 1 (A, B), FASTA
>7JKL_1 DNA-directed primase/polymerase protein (chains A, B)
MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKE
DVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKP
ANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFK
DNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATE
ESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGK
RVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Sequence of entity 2 (C, G), FASTA
>7JKL_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
>7JKL_3 DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*(DDG))-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

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