2OD8: Peptide derived from Cdc9

Structure of a peptide derived from Cdc9 bound to PCNA. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 May 2007.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 2,113
Mol. weight: 31.4 kDa
Released: 1 May 2007

Explore 2OD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OD8 contains 10 α-helices and 22 β-strands across 2 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	2-6	5	1
α-helix	9-17	9
β-strand	25-30	6	2
β-strand	35-40	6	2
β-strand	46-52	7	2
α-helix	54-56	3
β-strand	57-62	6	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	112-117	6	1
β-strand	135-140	6	2
α-helix	141-151	11
β-strand	157-163	7	3
β-strand	166-172	7	3
β-strand	177-182	6	3
β-strand	185	1	4
α-helix	191-193	3
β-strand	195	1	4
β-strand	196-199	4	2
β-strand	203-208	6	3
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	2
β-strand	235-241	7	2
β-strand	244-250	7	2
β-strand	253-254	2	5

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	36	1
β-strand	37-38	2	5
α-helix	39	1
α-helix	41-44	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A	protein	258	Saccharomyces cerevisiae	P15873 (AlphaFold model)
DNA ligase I, mitochondrial precursor	B	protein	22		P04819 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2OD8_1 Proliferating cell nuclear antigen (chains A)
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEY
RCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMD
IDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSV
IIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE

Sequence of entity 2 (B), FASTA

>2OD8_2 DNA ligase I, mitochondrial precursor (chains B)
AGKKPKQATLARFFTSMKNKPT

Primary citation

The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Vijayakumar, S., Chapados, B.R., Schmidt, K.H. et al. Nucleic Acids Res (2007) 35:1624-1637. DOI 10.1093/nar/gkm006 · PubMed

Other PDB entries of the same protein (UniProt P15873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V7M 1.93 Å, PCNA mutant L126A/I128A Protein Defective in Gene Silencing
8DQX 2.1 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR1 2.14 Å, Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
8DR3 2.2 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
1PLQ 2.3 Å, Crystal structure of the eukaryotic DNA polymerase processivity factor pcna
8DR6 2.39 Å, Closed state of RFC:PCNA bound to a nicked dsDNA
8DR0 2.42 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR4 2.45 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
3GPN 2.5 Å, Structure of the non-trimeric form of the E113G PCNA mutant protein
3V60 2.6 Å, Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164
8THW 2.6 Å, Cac1 PIP motif bound to PCNA
6W9W 2.65 Å, R80A PCNA mutant defective in BIR

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