3Q8M: Human Flap Endonuclease FEN1

Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Apr 2011.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,859
Mol. weight: 99.57 kDa
Released: 27 Apr 2011

Explore 3Q8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3Q8M contains 50 α-helices and 22 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: 25 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-21	4	1
α-helix	23-26	4
β-strand	30-34	5	1
α-helix	35-45	11
β-strand	47	1	2
β-strand	52	1	2
α-helix	53	1
β-strand	54	1	3
β-strand	60	1	3
α-helix	62-76	15
β-strand	80-85	6	1
α-helix	89-90	2
α-helix	91-93	3
α-helix	94-115	22
α-helix	120-129	10
α-helix	135-148	14
β-strand	152-154	3	1
α-helix	159-168	10
β-strand	174-176	3	1
α-helix	181-184	4
β-strand	189-192	4	1
α-helix	203	1
β-strand	204-208	5	1
α-helix	209-216	8
α-helix	220-231	12
α-helix	243-253	11
α-helix	256-262	7
α-helix	269-271	3
α-helix	276-284	9
α-helix	295-296	2
α-helix	303-306	4
α-helix	307-313	7
α-helix	314	1
α-helix	318-333	16

Chain B: 25 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-21	4	4
α-helix	23-26	4
β-strand	30-34	5	4
α-helix	35-45	11
β-strand	47-48	2	5
β-strand	51-52	2	5
α-helix	53	1
β-strand	54	1	6
β-strand	60	1	6
α-helix	62-76	15
β-strand	80-85	6	4
α-helix	89-90	2
α-helix	91-93	3
α-helix	94-115	22
α-helix	120-129	10
α-helix	135-148	14
β-strand	152-154	3	4
α-helix	159-168	10
β-strand	174-176	3	4
α-helix	181-184	4
β-strand	189-192	4	4
α-helix	203	1
β-strand	204-208	5	4
α-helix	209-216	8
α-helix	220-231	12
α-helix	243-253	11
α-helix	256-262	7
α-helix	269-271	3
α-helix	276-284	9
α-helix	295-296	2
α-helix	303-306	4
α-helix	307-313	7
α-helix	314	1
α-helix	318-333	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Flap endonuclease 1	A, B	protein	341	Homo sapiens	P39748 (AlphaFold model)
DNA (5'-d(apcptpcptpgpcpcptpcpapapgpapcpgpgpt)-3')	D, G	DNA	18
DNA (5'-d(tptpgpapgpgpcpapgpapgpt)-3')	E, H	DNA	12
DNA (5'-d(apcpcpgptpcp*c)-3')	F, I	DNA	7

Sequence of entity 1 (A, B), FASTA

>3Q8M_1 Flap endonuclease 1 (chains A, B)
GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT
SHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ
EVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMA
CLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGI
GPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEP
NEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ

Sequence of entity 2 (D, G), FASTA

>3Q8M_2 DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3') (chains D, G)
ACTCTGCCTCAAGACGGT

Sequence of entity 3 (E, H), FASTA

>3Q8M_3 DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3') (chains E, H)
TTGAGGCAGAGT

Sequence of entity 4 (F, I), FASTA

>3Q8M_4 DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3') (chains F, I)
ACCGTCC

Primary citation

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily. Tsutakawa, S.E., Classen, S., Chapados, B.R. et al. Cell (2011) 145:198-211. DOI 10.1016/j.cell.2011.03.004 · PubMed

Other PDB entries of the same protein (UniProt P39748 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RCI 1.66 Å, Crystal Structure of Flap Endonuclease FEN1 with Compound 28
1U7B 1.88 Å, Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
5ZOD 1.9 Å, Crystal Structure of hFen1 in apo form
5ZOE 1.95 Å, Crystal Structure of D181A hFen1 in complex with DNA
5E0V 2.07 Å, Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
5K97 2.1 Å, Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+
5KSE 2.1 Å, Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and Sm3+
9RDI 2.1 Å, Crystal Structure of Flap Endonuclease FEN1 with Compound 5
3Q8K 2.2 Å, Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap…
5ZOF 2.25 Å, Crystal Structure of D181A/R192F hFen1 in complex with DNA
5ZOG 2.3 Å, Crystal Structure of R192F hFen1 in complex with DNA
3Q8L 2.32 Å, Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap…

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