5YDR: DNMT1 RFTS domain

Structure of DNMT1 RFTS domain in complex with ubiquitin. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,340
Mol. weight: 45.24 kDa
Ligands: ZN, PO4
Released: 21 Feb 2018

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

Secondary structure: helices and β-sheets

5YDR contains 22 α-helices and 29 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	12-17	6	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
β-strand	66-71	6	1

Chain B: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	352	1	3
β-strand	359	1	3
α-helix	363-365	3
β-strand	366	1	4
α-helix	369-370	2
β-strand	375	1	5
α-helix	377-381	5
α-helix	384-386	3
β-strand	404-409	6	5
β-strand	410	1	6
β-strand	411-414	4	5
β-strand	418	1	4
β-strand	419	1	5
β-strand	433-440	8	5
β-strand	453-458	6	5
β-strand	463-467	5	5
β-strand	476-480	5	5
β-strand	485-488	4	5
α-helix	490	1
β-strand	491	1	6
α-helix	492	1
α-helix	496-501	6
α-helix	503-518	16
α-helix	524-533	10
α-helix	534-537	4
α-helix	542-545	4
α-helix	547-552	6
α-helix	554-567	14
α-helix	579-588	10
α-helix	592-597	6

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	7
β-strand	12-17	6	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	56-59	4
β-strand	66-71	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B	A, D	protein	75	Homo sapiens	P0CG47 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 1	B	protein	250	Homo sapiens	P26358 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5YDR_1 Polyubiquitin-B (chains A, D)
AHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRL

Sequence of entity 2 (B), FASTA

>5YDR_2 DNA (cytosine-5)-methyltransferase 1 (chains B)
MPKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTC
FSVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGF
DGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLIN
KIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAG
VTLGQRRAQA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PO4	Phosphate ion	O4 P	2

Primary citation

Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation. Li, T., Wang, L., Du, Y. et al. Nucleic Acids Res (2018) 46:3218-3231. DOI 10.1093/nar/gky104 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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