5UM9: Flap endonuclease 1

Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+. Determined by X-ray diffraction at 2.81 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,529
Mol. weight: 52.1 kDa
Ligands: SM
Released: 28 Jun 2017

Explore 5UM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UM9 contains 26 α-helices and 11 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: 26 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-20	3	1
α-helix	23-26	4
β-strand	29-34	6	1
α-helix	35-45	11
β-strand	47-48	2	2
β-strand	51-52	2	2
β-strand	54	1	3
β-strand	60	1	3
α-helix	62-76	15
β-strand	79-85	7	1
α-helix	89-90	2
α-helix	91-93	3
α-helix	94-108	15
α-helix	110-113	4
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	180-182	3
β-strand	189-192	4	1
α-helix	203-204	2
β-strand	205-208	4	1
α-helix	209-216	8
α-helix	220-231	12
α-helix	243-253	11
α-helix	256-260	5
α-helix	269-271	3
α-helix	276-284	9
α-helix	295-296	2
α-helix	299-301	3
α-helix	303-306	4
α-helix	307-313	7
α-helix	318-335	18
α-helix	337-339	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Flap endonuclease 1	A	protein	341	Homo sapiens	P39748 (AlphaFold model)
DNA (5'-d(apcptpcptpgpcpcptpcpapapgpapcpgpgpt)-3')	D	DNA	18	synthetic construct
DNA (5'-d(ptpcptptpgpapgpgpcpapgpapgpt)-3')	E	DNA	17	synthetic construct
DNA (5'-d(apcpcpgptpcp*c)-3')	F	DNA	7	synthetic construct

Sequence of entity 1 (A), FASTA

>5UM9_1 Flap endonuclease 1 (chains A)
GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT
SHLMGMFYRTIRMMENGIKPVYVFNGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ
EVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMD
CLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGI
GPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEP
NEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ

Sequence of entity 2 (D), FASTA

>5UM9_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)
ACTCTGCCTCAAGACGGT

Sequence of entity 3 (E), FASTA

>5UM9_3 DNA (5'-D(P*TP*CP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3') (chains E)
ATATCTTGAGGCAGAGT

Sequence of entity 4 (F), FASTA

>5UM9_4 DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3') (chains F)
ACCGTCC

Ligands and cofactors

ID	Name	Formula	Copies
SM	Samarium (III) ion	Sm	5

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

Primary citation

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Tsutakawa, S.E., Thompson, M.J., Arvai, A.S. et al. Nat Commun (2017) 8:15855-15855. DOI 10.1038/ncomms15855 · 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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