8YJQ: Human endogenous PCNA-FEN1 complex - State C

Structure of the human endogenous PCNA-FEN1 complex - State C. Determined by electron microscopy at 3.51 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.51 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,856
Mol. weight: 147.07 kDa
Released: 4 Dec 2024

Explore 8YJQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YJQ contains 46 α-helices and 71 β-strands across 4 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
α-helix	10-19	10
β-strand	25-30	6	6
β-strand	34-40	7	6
β-strand	46-53	8	6
β-strand	59-61	3	5
β-strand	66-71	6	6
α-helix	72-79	8
β-strand	87-92	6	5
β-strand	99-104	6	5
β-strand	110-116	7	5
α-helix	123-125	3
β-strand	135-140	6	6
α-helix	141-151	11
β-strand	157-160	4	7
β-strand	166-168	3	8
β-strand	169-170	2	7
β-strand	171	1	8
β-strand	176-183	8	8
α-helix	191-193	3
β-strand	196-197	2	6
β-strand	205-208	4	7
α-helix	210-215	6
α-helix	216-218	3
β-strand	224-229	6	6
β-strand	235-240	6	6
β-strand	246-251	6	6

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
α-helix	10-19	10
β-strand	25-30	6	11
β-strand	34-40	7	11
β-strand	46-53	8	11
β-strand	59-60	2	8
β-strand	66-71	6	11
α-helix	72-79	8
β-strand	87-92	6	8
β-strand	98-104	7	8
β-strand	110-117	8	8
α-helix	128-130	3
β-strand	135-140	6	11
α-helix	141-151	11
β-strand	157-162	6	9
β-strand	167-172	6	9
β-strand	176-181	6	9
β-strand	196-199	4	11
β-strand	204-208	5	9
α-helix	210-215	6
β-strand	224-229	6	11
α-helix	234	1
β-strand	235-239	5	11
β-strand	246-251	6	11

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
α-helix	10-16	7
β-strand	25-30	6	10
β-strand	34-40	7	10
β-strand	47-53	7	10
β-strand	59-61	3	9
β-strand	66-71	6	10
α-helix	72-79	8
β-strand	87-92	6	9
β-strand	98-104	7	9
β-strand	111-117	7	9
β-strand	119	1	10
α-helix	123	1
β-strand	124-127	4	4
β-strand	135-140	6	10
α-helix	141-151	11
β-strand	157-163	7	5
β-strand	166-172	7	5
β-strand	176-182	7	5
β-strand	196-198	3	10
β-strand	204	1	5
β-strand	207-208	2	5
α-helix	209-215	7
β-strand	224-230	7	10
β-strand	233-241	9	10
β-strand	245-251	7	10
α-helix	252-253	2
β-strand	254-255	2	3

Chain D: 27 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	15-17	3
β-strand	18-21	4	1
β-strand	31-34	4	1
α-helix	35-44	10
β-strand	54	1	2
β-strand	60	1	2
α-helix	62-76	15
β-strand	81-85	5	1
α-helix	86	1
α-helix	89-90	2
α-helix	94-117	24
α-helix	120-126	7
α-helix	127-130	4
α-helix	136-139	4
α-helix	142-148	7
β-strand	152-154	3	1
α-helix	159-168	10
β-strand	174-176	3	1
α-helix	181-185	5
β-strand	189-192	4	1
β-strand	204-208	5	1
α-helix	209-216	8
α-helix	220-229	10
α-helix	244-252	9
α-helix	257-260	4
α-helix	269-271	3
α-helix	276-284	9
α-helix	288-290	3
α-helix	299-301	3
α-helix	305-306	2
α-helix	307-311	5
α-helix	318-329	12
α-helix	335	1
β-strand	336-337	2	3
α-helix	338-339	2
α-helix	340-342	3
β-strand	345-349	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Flap endonuclease 1	D	protein	380	Homo sapiens	P39748 (AlphaFold model)
Proliferating cell nuclear antigen	A, B, C	protein	261	Homo sapiens	P12004 (AlphaFold model)
upstream DNA	J	DNA	17	Homo sapiens
parent strand	E	DNA	28	Homo sapiens
downstream DNA	F	DNA	10	Homo sapiens
5 prime flap DNA	H	DNA	4	Homo sapiens

Sequence of entity 1 (D), FASTA

>8YJQ_1 Flap endonuclease 1 (chains D)
MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGET
TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE
QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM
DCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG
IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSE
PNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEP
KGSTKKKAKTGAAGKFKRGK

Sequence of entity 2 (A, B, C), FASTA

>8YJQ_2 Proliferating cell nuclear antigen (chains A, B, C)
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY
RCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD
LDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI
KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYK
IADMGHLKYYLAPKIEDEEGS

Sequence of entity 3 (J), FASTA

>8YJQ_3 upstream DNA (chains J)
TTTTTTTTTAATAATTT

Sequence of entity 4 (E), FASTA

>8YJQ_4 parent strand (chains E)
ATTAAAAATTATAATTATTAAAAAAAAA

Sequence of entity 5 (F), FASTA

>8YJQ_5 downstream DNA (chains F)
AATTTTTAAT

Sequence of entity 6 (H), FASTA

>8YJQ_6 5 prime flap DNA (chains H)
TTAT

Primary citation

Structural insight into Okazaki fragment maturation mediated by PCNA-bound FEN1 and RNaseH2. Tian, Y., Li, N., Li, Q. et al. EMBO J (2025) 44:484-504. DOI 10.1038/s44318-024-00296-x · 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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