8YJR: Human endogenous PCNA-FEN1 complex - State D

Structure of the human endogenous PCNA-FEN1 complex - State D. 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: 9,962
Mol. weight: 148.92 kDa
Released: 4 Dec 2024

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

Secondary structure: helices and β-sheets

8YJR contains 43 α-helices and 72 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	10-18	9
β-strand	25-30	6	10
β-strand	34-40	7	10
β-strand	46-53	8	10
α-helix	54-56	3
β-strand	60-61	2	6
β-strand	67-71	5	10
α-helix	72-79	8
β-strand	87-91	5	6
β-strand	98	1	11
β-strand	100-104	5	6
β-strand	110-114	5	6
β-strand	117	1	11
β-strand	119	1	10
α-helix	127-129	3
β-strand	135-140	6	10
α-helix	141-152	12
β-strand	158-161	4	1
β-strand	168-171	4	1
β-strand	178-182	5	1
β-strand	196-199	4	10
β-strand	204-206	3	1
α-helix	210-215	6
α-helix	216-218	3
β-strand	224-229	6	10
β-strand	235-241	7	10
β-strand	245-251	7	10

Chain B: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	10-19	10
β-strand	25-30	6	2
β-strand	34-40	7	2
β-strand	47-53	7	2
β-strand	59-61	3	1
β-strand	66-71	6	2
α-helix	72-79	8
β-strand	87-91	5	1
β-strand	100-104	5	1
β-strand	110-114	5	1
β-strand	135-140	6	2
α-helix	141-151	11
β-strand	157-161	5	3
β-strand	166-172	7	3
β-strand	177-183	7	3
β-strand	196-199	4	2
β-strand	204-208	5	3
α-helix	210-216	7
β-strand	224-229	6	2
α-helix	234-235	2
β-strand	236-239	4	2
β-strand	246-250	5	2

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
α-helix	9-19	11
β-strand	25-30	6	4
β-strand	34-40	7	4
β-strand	46-53	8	4
β-strand	59-62	4	3
β-strand	66-71	6	4
α-helix	72-79	8
α-helix	86	1
β-strand	87-92	6	3
β-strand	98-104	7	3
β-strand	110-117	8	3
β-strand	123-127	5	5
α-helix	128-129	2
β-strand	135-140	6	4
α-helix	141-152	12
β-strand	157-162	6	6
β-strand	167-172	6	6
β-strand	177-182	6	6
β-strand	196-198	3	4
β-strand	204-208	5	6
α-helix	210-215	6
β-strand	224-230	7	4
β-strand	233-240	8	4
β-strand	246-251	6	4
α-helix	252-253	2
β-strand	254	1	6

Chain D: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-21	4	7
α-helix	23-25	3
β-strand	30-34	5	7
α-helix	35-45	11
β-strand	47	1	8
β-strand	52	1	8
β-strand	54	1	9
β-strand	60	1	9
α-helix	62-75	14
β-strand	80-85	6	7
α-helix	86	1
α-helix	89-90	2
α-helix	91-93	3
α-helix	94-115	22
α-helix	120-129	10
α-helix	135-147	13
β-strand	152-154	3	7
α-helix	159-168	10
β-strand	174-176	3	7
α-helix	181-185	5
β-strand	189-191	3	7
β-strand	204-208	5	7
α-helix	209-215	7
α-helix	220-229	10
α-helix	243-252	10
α-helix	256-261	6
α-helix	270-271	2
α-helix	276-284	9
α-helix	300-302	3
α-helix	304-311	8
α-helix	318-332	15
α-helix	335-336	2
β-strand	337	1	6
α-helix	338	1
β-strand	345-350	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, B, C	protein	261	Homo sapiens	P12004 (AlphaFold model)
Flap endonuclease 1	D	protein	380	Homo sapiens	P39748 (AlphaFold model)
upstream DNA	J	DNA	20	Homo sapiens
parent DNA	E	DNA	31	Homo sapiens
downstream DNA	F	DNA	11	Homo sapiens
5 prime flap DNA	H	DNA	3	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>8YJR_1 Proliferating cell nuclear antigen (chains A, B, C)
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY
RCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD
LDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI
KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYK
IADMGHLKYYLAPKIEDEEGS

Sequence of entity 2 (D), FASTA

>8YJR_2 Flap endonuclease 1 (chains D)
MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGET
TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE
QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM
DCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG
IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSE
PNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEP
KGSTKKKAKTGAAGKFKRGK

Sequence of entity 3 (J), FASTA

>8YJR_3 upstream DNA (chains J)
TATATTTTTTTTAAATTTAT

Sequence of entity 4 (E), FASTA

>8YJR_4 parent DNA (chains E)
TTTTTTTATAAATAAATTTAAAAAAAATATA

Sequence of entity 5 (F), FASTA

>8YJR_5 downstream DNA (chains F)
TTATAAAAAAA

Sequence of entity 6 (H), FASTA

>8YJR_6 5 prime flap DNA (chains H)
TTT

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 P12004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7B 1.88 Å, Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
8F5Q 1.9 Å, Crystal structure of human PCNA in complex with the PIP box of FBH1
9N3L 1.9 Å, Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112
5E0U 1.93 Å, Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
5MLO 1.96 Å, Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide
4RJF 2.01 Å, Crystal structure of the human sliding clamp at 2.0 angstrom resolution
5E0V 2.07 Å, Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
3VKX 2.1 Å, Structure of PCNA
6HVO 2.1 Å, Crystal structure of human PCNA in complex with three peptides of p12 subunit of human…
4ZTD 2.2 Å, Crystal Structure of Human PCNA in complex with a TRAIP peptide
5YCO 2.2 Å, Complex structure of PCNA with UHRF2
5MOM 2.27 Å, Crystal Structure of PCNA encoding the hypomorphic mutation S228I

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