5V7M: Proliferating cell nuclear antigen

PCNA mutant L126A/I128A Protein Defective in Gene Silencing. Determined by X-ray diffraction at 1.93 Å resolution. Released 14 Mar 2018.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 1
Atoms: 2,115
Mol. weight: 29.84 kDa
Ligands: MG
Released: 14 Mar 2018

Explore 5V7M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V7M contains 7 α-helices and 20 β-strands across 1 chain. 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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	59-62	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	111-117	7	1
β-strand	135-140	6	2
α-helix	141-152	12
β-strand	157-163	7	3
β-strand	166-173	8	3
β-strand	176-182	7	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A	protein	265	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P15873 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V7M_1 Proliferating cell nuclear antigen (chains A)
MHHHHHHMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIG
VEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAE
YSLKLMDIDADFAKAEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADG
DIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEA
PALFQFDLKSGFLQFFLAPKFNDEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring. Kondratick, C.M., Litman, J.M., Shaffer, K.V. et al. PLoS One (2018) 13:e0193333-e0193333. DOI 10.1371/journal.pone.0193333 · PubMed

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

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
4L6P 2.68 Å, Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair

Browse structure collections

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