6EHT: Proliferating cell nuclear antigen

Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme. Determined by X-ray diffraction at 3.2 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 7
Atoms: 5,925
Mol. weight: 95.17 kDa
Released: 8 Aug 2018

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

Secondary structure: helices and β-sheets

6EHT contains 26 α-helices and 61 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-20	11
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	67-71	5	2
α-helix	72-81	10
β-strand	87-92	6	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	166-172	7	3
β-strand	176-183	8	3
α-helix	184-185	2
β-strand	196-197	2	2
β-strand	203-208	6	3
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-230	7	2
β-strand	233-241	9	2
β-strand	245-251	7	2

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	4
α-helix	10-20	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	60-61	2	4
β-strand	67-71	5	5
α-helix	72-81	10
β-strand	87-91	5	4
β-strand	98-104	7	4
β-strand	110-117	8	4
β-strand	119	1	5
β-strand	127	1	6
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	196-197	2	5
β-strand	203-208	6	1
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-230	7	5
β-strand	233-241	9	5
β-strand	245-251	7	5

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	3
α-helix	10-20	11
β-strand	25-31	7	7
β-strand	34-40	7	7
β-strand	47-53	7	7
α-helix	54-56	3
β-strand	59-62	4	3
β-strand	66-71	6	7
α-helix	72-81	10
β-strand	87-93	7	3
β-strand	98-104	7	3
β-strand	110-117	8	3
β-strand	119	1	7
β-strand	127	1	8
β-strand	135-140	6	7
α-helix	141-152	12
β-strand	157-162	6	4
β-strand	166-172	7	4
β-strand	176-183	8	4
α-helix	184-185	2
β-strand	196-197	2	7
β-strand	203-208	6	4
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-230	7	7
β-strand	233-241	9	7
β-strand	245-251	7	7

Chains D and E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	62-64	3
α-helix	65-67	3
β-strand	70	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	A, B	protein	254	Homo sapiens	P12004 (AlphaFold model)
Proliferating cell nuclear antigen	C	protein	256	Homo sapiens	P12004 (AlphaFold model)
PCNA-associated factor	D, E	protein	20	Homo sapiens	Q15004 (AlphaFold model)
DNA (5'-d(paptpapcpgpaptpgpgpg)-3')	F	DNA	10	Homo sapiens
DNA (5'-d(pcpcpcpaptpcpgptpapt)-3')	G	DNA	10	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6EHT_1 Proliferating cell nuclear antigen (chains A, B)
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY
RCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD
LDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI
KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYK
IADMGHLKYYLAPK

Sequence of entity 2 (C), FASTA

>6EHT_2 Proliferating cell nuclear antigen (chains C)
HMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDT
YRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLM
DLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGN
IKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEY
KIADMGHLKYYLAPKI

Sequence of entity 3 (D, E), FASTA

>6EHT_3 PCNA-associated factor (chains D, E)
PVCVRPTPKWQKGIGEFFRL

Sequence of entity 4 (F), FASTA

>6EHT_4 DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3') (chains F)
ATACGATGGG

Sequence of entity 5 (G), FASTA

>6EHT_5 DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3') (chains G)
CCCATCGTAT

Primary citation

p15PAF binding to PCNA modulates the DNA sliding surface. De March, M., Barrera-Vilarmau, S., Crespan, E. et al. Nucleic Acids Res (2018) 46:9816-9828. DOI 10.1093/nar/gky723 · 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

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