5E0V: Human PCNA variant

Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms. Determined by X-ray diffraction at 2.07 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,129
Mol. weight: 61.19 kDa
Released: 20 Apr 2016

Explore 5E0V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E0V contains 17 α-helices and 44 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-22	13
β-strand	25-30	6	2
β-strand	34-40	7	2
β-strand	46-53	8	2
α-helix	54-56	3
β-strand	59-62	4	1
β-strand	66-71	6	2
α-helix	72-80	9
α-helix	86	1
β-strand	87-92	6	1
β-strand	98-104	7	1
β-strand	111-117	7	1
β-strand	125	1	3
α-helix	129-131	3
β-strand	135-140	6	2
α-helix	141-154	14
β-strand	157-162	6	4
β-strand	167-172	6	4
β-strand	177-182	6	4
β-strand	196-199	4	2
β-strand	204-208	5	4
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	2
β-strand	235-240	6	2
β-strand	245-251	7	2
β-strand	254	1	5

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	10-22	13
β-strand	25-31	7	7
β-strand	34-40	7	7
β-strand	46-53	8	7
α-helix	54-56	3
β-strand	59-62	4	6
β-strand	66-71	6	7
α-helix	72-80	9
β-strand	87-92	6	6
β-strand	98-104	7	6
β-strand	111-117	7	6
β-strand	127	1	8
α-helix	128-132	5
β-strand	135-140	6	7
α-helix	141-154	14
β-strand	157-162	6	9
β-strand	167-172	6	9
β-strand	177-182	6	9
β-strand	196-199	4	7
β-strand	204-208	5	9
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	7
β-strand	235-240	6	7
β-strand	245-251	7	7
β-strand	254	1	10

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	337	1	5
α-helix	340-342	3
β-strand	347	1	3

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	337	1	10
α-helix	340-342	3
β-strand	345	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, B	protein	261	Homo sapiens	P12004 (AlphaFold model)
Flap endonuclease 1	C, D	protein	16	Homo sapiens	P39748 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5E0V_1 Proliferating cell nuclear antigen (chains A, B)
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY
RCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD
LDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI
KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLIMSADVPLVVEYK
IADMGHLKYYLAPKIEDEEGS

Sequence of entity 2 (C, D), FASTA

>5E0V_2 Flap endonuclease 1 (chains C, D)
STQGRLDDFFKVTGSL

Primary citation

A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. Duffy, C.M., Hilbert, B.J., Kelch, B.A. J Mol Biol (2016) 428:1023-1040. DOI 10.1016/j.jmb.2015.11.029 · 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
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
1VYM 2.3 Å, Native human pcna

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