7U7L: DNA polymerase eta

Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mM Mg2+ for 300s with flipped-out product. Determined by X-ray diffraction at 1.47 Å resolution. Released 4 May 2022.

Method: X-ray diffraction
Resolution: 1.47 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 4,453
Mol. weight: 55.49 kDa
Ligands: DPO, MG
Released: 4 May 2022

Explore 7U7L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U7L contains 23 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.

Chain A: 23 helices, 20 β-strands

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	63-64	2	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	108-113	6	1
β-strand	116-120	5	1
α-helix	122-131	10
α-helix	135-138	4
α-helix	139-141	3
β-strand	145-147	3	1
α-helix	163-179	17
α-helix	185-208	24
β-strand	212-217	6	1
α-helix	220-229	10
β-strand	235-237	3	1
α-helix	240-242	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase eta	A	protein	435	Homo sapiens	Q9Y253 (AlphaFold model)
DNA (5'-d(cpaptptpaptpgpapcpgpcpt)-3')	T	DNA	12	synthetic construct
DNA (5'-d(apgpcpgptpcpaptp*g)-3')	P	DNA	9	synthetic construct

Sequence of entity 1 (A), FASTA

>7U7L_1 DNA polymerase eta (chains A)
GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAF
GVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEA
YVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDS
LQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTL
VSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSW
LYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRN
DNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSP
PLTMLFLCATKFSAS

Sequence of entity 2 (T), FASTA

>7U7L_2 DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') (chains T)
CATTATGACGCT

Sequence of entity 3 (P), FASTA

>7U7L_3 DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3') (chains P)
AGCGTCATG

Ligands and cofactors

ID	Name	Formula	Copies
DPO	Diphosphate	O7 P2	1
MG	Magnesium ion	Mg	1

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

Primary citation

In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Chang, C., Lee Luo, C., Gao, Y. Nat Commun (2022) 13:2346-2346. DOI 10.1038/s41467-022-30005-3 · PubMed

Other PDB entries of the same protein (UniProt Q9Y253 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M7N 1.31 Å, Human DNA Pol eta with 2'-FA-ended primer and dAMPNPP
5KFZ 1.44 Å, Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s…
5KFN 1.45 Å, Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 1 mM…
5KFS 1.46 Å, Human DNA polymerase eta R61A-DNA ternary complex: ground state at pH7.0 (K+ MES) with 1…
7M7M 1.46 Å, Human DNA Pol eta with rA-ended primer and dAMPNPP
7M7T 1.46 Å, Human DNA Pol eta S113A with dT-ended primer and dATP: in crystallo reaction for 0 s
7M84 1.47 Å, Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 40 s
4ECQ 1.5 Å, Human DNA polymerase eta- DNA ternary complex: AT crystal at pH6.8(K+ MES) with 1 Ca2+ ion
5KFC 1.5 Å, Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 180s
5KFA 1.51 Å, Human DNA polymerase eta-DNA ternary complex: ground state at pH7.0 (K+ MES) with 1 Ca2+…
5KFO 1.52 Å, Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 1 mM…
5KFT 1.52 Å, Human DNA polymerase eta R61A-DNA ternary complex: reaction with 1 mM Mg2+ for 40s

Browse structure collections

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