6K3A: Human PCNA

Crystal structure of human PCNA in complex with DNMT1 PIP box motif. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,671
Mol. weight: 93.68 kDa
Released: 26 Jun 2019

Explore 6K3A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K3A contains 33 α-helices and 81 β-strands across 6 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.

Chains A and E: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-19	10
β-strand	25-31	7	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	72-79	8
β-strand	87-92	6	1
β-strand	98-104	7	1
β-strand	110	1	3
β-strand	111-117	7	1
α-helix	118	1
β-strand	119	1	2
α-helix	120	1
β-strand	127	1	4
α-helix	128-130	3
β-strand	135-140	6	2
α-helix	141-152	12
β-strand	157-161	5	5
β-strand	167	1	6
β-strand	168-170	3	5
β-strand	171-172	2	7
β-strand	176-178	3	7
β-strand	182	1	6
β-strand	196-199	4	2
β-strand	204-208	5	5
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	2
β-strand	235-241	7	2
β-strand	245-251	7	2
α-helix	252-253	2
β-strand	254-255	2	5

Chains B, D and F: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	163-164	2	5
α-helix	167-169	3
β-strand	172	1	4

Chain C: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
α-helix	10-19	10
β-strand	25-31	7	8
β-strand	34-40	7	8
β-strand	46-53	8	8
α-helix	54-56	3
β-strand	59-62	4	7
β-strand	66-71	6	8
α-helix	72-79	8
β-strand	87-92	6	7
β-strand	98-104	7	7
β-strand	110	1	6
β-strand	111-117	7	7
α-helix	118	1
β-strand	119	1	8
α-helix	120	1
β-strand	127	1	9
α-helix	128-130	3
β-strand	135-140	6	8
α-helix	141-152	12
β-strand	157-161	5	10
β-strand	167	1	11
β-strand	168-170	3	10
β-strand	171-173	3	12
β-strand	176-178	3	12
β-strand	182	1	11
β-strand	196-199	4	8
β-strand	204-208	5	10
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	8
β-strand	235-241	7	8
β-strand	245-251	7	8
α-helix	252-253	2
β-strand	254-255	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, C, E	protein	264	Homo sapiens	P12004 (AlphaFold model)
Peptide from DNA (cytosine-5)-methyltransferase 1	B, D, F	protein	20	Homo sapiens	P26358 (AlphaFold model)

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

>6K3A_1 Proliferating cell nuclear antigen (chains A, C, E)
GPGMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGF
DTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMK
LMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGN
GNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVV
EYKIADMGHLKYYLAPKIEDEEGS

Sequence of entity 2 (B, D, F), FASTA

>6K3A_2 Peptide from DNA (cytosine-5)-methyltransferase 1 (chains B, D, F)
STRQTTITSHFAKGPAKRKP

Primary citation

Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction. Jimenji, T., Matsumura, R., Kori, S. et al. Biochem Biophys Res Commun (2019) 516:578-583. DOI 10.1016/j.bbrc.2019.06.060 · 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

Browse structure collections

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