Human DNA polymerase eta-DNA-gemC-ended primer-dAMPNPP ternary complex with Mg2+. Determined by X-ray diffraction at 1.52 Å resolution. Released 15 May 2024.
Explore 8V7G in 3D Show helices and sheets RCSB PDB PDBe
8V7G contains 22 α-helices and 20 β-strands across 1 chain. 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 9-14 | 6 | 1 |
| α-helix | 17-25 | 9 | |
| α-helix | 27-29 | 3 | |
| β-strand | 34-38 | 5 | 2 |
| β-strand | 46-50 | 5 | 2 |
| α-helix | 52-55 | 4 | |
| β-strand | 64 | 1 | 2 |
| α-helix | 65-71 | 7 | |
| β-strand | 76-79 | 4 | 2 |
| α-helix | 80-81 | 2 | |
| β-strand | 82-83 | 2 | 3 |
| β-strand | 86-87 | 2 | 3 |
| α-helix | 90-106 | 17 | |
| β-strand | 109-113 | 5 | 1 |
| β-strand | 116-120 | 5 | 1 |
| α-helix | 122-132 | 11 | |
| α-helix | 135-138 | 4 | |
| α-helix | 139-141 | 3 | |
| β-strand | 145-147 | 3 | 1 |
| α-helix | 163-176 | 14 | |
| α-helix | 186-208 | 23 | |
| β-strand | 212-217 | 6 | 1 |
| α-helix | 220-229 | 10 | |
| β-strand | 235-237 | 3 | 1 |
| α-helix | 243-248 | 6 | |
| β-strand | 251 | 1 | 4 |
| α-helix | 252-254 | 3 | |
| α-helix | 261-270 | 10 | |
| β-strand | 274 | 1 | 4 |
| α-helix | 275-280 | 6 | |
| α-helix | 283-290 | 8 | |
| α-helix | 292-301 | 10 | |
| β-strand | 313 | 1 | 1 |
| β-strand | 319-324 | 6 | 5 |
| α-helix | 327-329 | 3 | |
| β-strand | 331-333 | 3 | 5 |
| α-helix | 334-359 | 26 | |
| β-strand | 361-372 | 12 | 5 |
| β-strand | 381-386 | 6 | 5 |
| α-helix | 392-403 | 12 | |
| α-helix | 404-406 | 3 | |
| β-strand | 414-431 | 18 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| DNA polymerase eta | A | protein | 435 | Homo sapiens | Q9Y253 (AlphaFold model) |
| DNA (5'-d(*cp*ap*tp*tp*gp*tp*gp*ap*cp*gp*cp*t)-3') | T | DNA | 12 | synthetic construct | |
| DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(U7B))-3') | P | DNA | 8 | synthetic construct |
>8V7G_1 DNA polymerase eta (chains A) GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAF GVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEA YVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDS LQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTL VSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSW LYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRN DNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSP PLTMLFLCATKFSAS
>8V7G_2 DNA (5'-D(*CP*AP*TP*TP*GP*TP*GP*AP*CP*GP*CP*T)-3') (chains T) CATTGTGACGCT
>8V7G_3 DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(U7B))-3') (chains P) AGCGTCAC
| ID | Name | Formula | Copies |
|---|---|---|---|
| DZ4 | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphory… | C10 H17 N6 O11 P3 | 1 |
| MG | Magnesium ion | Mg | 2 |
Water and common crystallization additives (GOL) are not listed.
Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol eta catalyzed DNA synthesis. Chang, C., Zhou, G., Lee Luo, C. et al. J Biol Chem (2024) 300:107361-107361. DOI 10.1016/j.jbc.2024.107361 · PubMed
Other PDB entries of the same protein (UniProt Q9Y253 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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