3V60: Ubiquitin-like protein SMT3

Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164. Determined by X-ray diffraction at 2.6 Å resolution. Released 29 Feb 2012.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 2,776
Mol. weight: 39.17 kDa
Released: 29 Feb 2012

Explore 3V60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V60 contains 10 α-helices and 25 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: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	23-29	7	1
β-strand	34-40	7	1
α-helix	46-56	11
β-strand	64-67	4	1
β-strand	70-72	3	1
β-strand	88-92	5	1

Chain B: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	2
α-helix	10-19	10
β-strand	25-31	7	3
β-strand	34-40	7	3
β-strand	46-53	8	3
α-helix	54-56	3
β-strand	57-62	6	2
β-strand	66-71	6	3
α-helix	72-79	8
β-strand	87-92	6	2
β-strand	98-104	7	2
β-strand	111-117	7	2
α-helix	118	1
β-strand	135-140	6	3
α-helix	141-152	12
β-strand	157-163	7	4
β-strand	166-172	7	4
β-strand	177-182	6	4
β-strand	185	1	5
α-helix	191-193	3
β-strand	195	1	5
β-strand	196-199	4	3
β-strand	203-208	6	4
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	3
β-strand	235-241	7	3
β-strand	244-250	7	3
α-helix	251-254	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein SMT3	A	protein	84	Saccharomyces cerevisiae	Q12306 (AlphaFold model)
Proliferating cell nuclear antigen	B	protein	258	Saccharomyces cerevisiae	P15873 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3V60_1 Ubiquitin-like protein SMT3 (chains A)
GSHMRPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQA
DQTPEDLDMEDNDIIEAHREQIGG

Sequence of entity 2 (B), FASTA

>3V60_2 Proliferating cell nuclear antigen (chains B)
MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEY
RCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMD
IDADFLGIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSV
IIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD
LKSGFLQFFLAPKFNDEE

Primary citation

Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Armstrong, A.A., Mohideen, F., Lima, C.D. Nature (2012) 483:59-63. DOI 10.1038/nature10883 · PubMed

Other PDB entries of the same protein (UniProt Q12306 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UF8 1.5 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A…
6UKZ 1.52 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 6
3UQA 1.55 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
3VAW 1.55 Å, Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface…
5YCA 1.57 Å, Crystal structure of inner membrane protein Bqt4 in complex with LEM2
7P7W 1.57 Å, N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with…
1EUV 1.6 Å, X-ray structure of the C-terminal ULP1 protease domain in complex with SMT3, the yeast…
6UKU 1.68 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 3
7P7I 1.7 Å, Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides
6UKM 1.74 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound MSA-2
4G50 1.75 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
7P9L 1.75 Å, N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with…

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