4ZTD: Human PCNA

Name: PDB 4ZTD: Crystal Structure of Human PCNA in complex with a TRAIP peptide
Published: 2015-12-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Crystal Structure of Human PCNA in complex with a TRAIP peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,245
Mol. weight: 86.92 kDa
Released: 16 Dec 2015

Explore 4ZTD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZTD contains 26 α-helices and 57 β-strands across 5 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	9-17	9
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	59-60	2	1
β-strand	66-71	6	2
α-helix	72-79	8
α-helix	86	1
β-strand	87-91	5	1
β-strand	98-104	7	1
β-strand	110-117	8	1
β-strand	119	1	2
α-helix	128-130	3
β-strand	135-140	6	2
α-helix	141-152	12
β-strand	157-162	6	3
β-strand	166-173	8	3
β-strand	176-183	8	3
α-helix	184-185	2
β-strand	196-199	4	2
β-strand	203-208	6	3
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

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	4
α-helix	9-17	9
β-strand	25-31	7	5
β-strand	34-40	7	5
β-strand	46-53	8	5
α-helix	54-56	3
β-strand	59-61	3	4
β-strand	66-71	6	5
α-helix	72-80	9
β-strand	87-92	6	4
β-strand	98-104	7	4
β-strand	110-117	8	4
α-helix	118	1
β-strand	119	1	5
β-strand	135-140	6	5
α-helix	141-152	12
β-strand	157-162	6	1
β-strand	166-172	7	1
β-strand	176-183	8	1
α-helix	184-185	2
β-strand	196-199	4	5
β-strand	203-208	6	1
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	5
β-strand	235-241	7	5
β-strand	245-251	7	5

Chain C: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
α-helix	9-20	12
β-strand	25-31	7	6
β-strand	34-40	7	6
β-strand	46-53	8	6
α-helix	54-56	3
β-strand	59-61	3	3
β-strand	66-71	6	6
α-helix	72-80	9
β-strand	87-91	5	3
β-strand	98-104	7	3
β-strand	110-117	8	3
β-strand	119	1	6
β-strand	135-140	6	6
α-helix	141-154	14
β-strand	157-162	6	4
β-strand	166-172	7	4
β-strand	176-183	8	4
β-strand	196-199	4	6
β-strand	203-208	6	4
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	6
β-strand	235-241	7	6
β-strand	245-251	7	6

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	463-465	3

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	460-462	3
α-helix	464-466	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, B, C	protein	253	Homo sapiens	P12004 (AlphaFold model)
Ala-phe-gln-ala-lys-leu-asp-thr-phe-leu-trp-ser	D, E	protein	12	Homo sapiens	Q9BWF2 (AlphaFold model)
Ala-gly-ala-gly-ala	F	protein	5	Homo sapiens

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

>4ZTD_1 Proliferating cell nuclear antigen (chains A, B, C)
FEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYR
CDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDL
DVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIK
LSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKI
ADMGHLKYYLAPK

Sequence of entity 2 (D, E), FASTA

>4ZTD_2 ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SER (chains D, E)
AFQAKLDTFLWS

Sequence of entity 3 (F), FASTA

>4ZTD_3 ALA-GLY-ALA-GLY-ALA (chains F)
AGAGA

Primary citation

TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress. Hoffmann, S., Smedegaard, S., Nakamura, K. et al. J Cell Biol (2016) 212:63-75. DOI 10.1083/jcb.201506071 · 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…
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

Browse structure collections

About this viewer

MolViewer shows 4ZTD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.