4L6P: Proliferating cell nuclear antigen

Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair. Determined by X-ray diffraction at 2.68 Å resolution. Released 1 Oct 2014.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 3
Atoms: 6,052
Mol. weight: 89.68 kDa
Released: 1 Oct 2014

Explore 4L6P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L6P contains 21 α-helices and 55 β-strands across 3 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	9-19	11
β-strand	25-31	7	2
β-strand	34-39	6	2
β-strand	46-53	8	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	86-92	7	1
β-strand	98-105	8	1
β-strand	111-117	7	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
α-helix	191-193	3
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	244-250	7	2

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	9-19	11
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	59-62	4	4
β-strand	66-71	6	5
α-helix	72-79	8
β-strand	87-92	6	4
β-strand	98-104	7	4
β-strand	111-117	7	4
β-strand	119	1	5
β-strand	135-140	6	5
α-helix	141-151	11
β-strand	157-163	7	6
β-strand	166-172	7	6
β-strand	177-182	6	6
β-strand	196-199	4	5
β-strand	203-208	6	6
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	5
α-helix	234	1
β-strand	235-241	7	5
β-strand	244-250	7	5

Chain C: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
α-helix	9-20	12
β-strand	25-31	7	8
β-strand	34-40	7	8
β-strand	46-52	7	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	111-117	7	7
β-strand	135-140	6	8
α-helix	141-151	11
β-strand	157-163	7	9
β-strand	166-172	7	9
β-strand	177-182	6	9
α-helix	191-193	3
β-strand	196-199	4	8
β-strand	203-208	6	9
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	8
β-strand	235-241	7	8
β-strand	244-250	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, B, C	protein	264	Saccharomyces cerevisiae S288c	P15873 (AlphaFold model)

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

>4L6P_1 Proliferating cell nuclear antigen (chains A, B, C)
HHHHHHMLEAKFEEASLFKRIIDGFKDYVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGV
EAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEY
SLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGD
IGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAP
ALFQFDLKSGFLQFFLAPKFNDEE

Primary citation

Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair. Dieckman, L.M., Boehm, E.M., Hingorani, M.M. et al. Biochemistry (2013) 52:5611-5619. DOI 10.1021/bi400378e · 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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