5WVO: DNMT1 RFTS domain

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3. Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,362
Mol. weight: 49.12 kDa
Ligands: ZN
Released: 15 Nov 2017

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

Secondary structure: helices and β-sheets

5WVO contains 18 α-helices and 32 β-strands across 4 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	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
α-helix	56-59	4
β-strand	66-71	6	1
β-strand	74	1	3

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	11	1	5
β-strand	12-16	5	4
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	6
β-strand	66-71	6	4

Chain C: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	367	1	7
β-strand	375	1	8
α-helix	377-381	5
α-helix	384-386	3
β-strand	392	1	5
α-helix	402-403	2
β-strand	404-409	6	8
β-strand	410	1	9
β-strand	411-414	4	8
β-strand	418	1	7
β-strand	419	1	8
β-strand	433-440	8	8
β-strand	453-458	6	8
β-strand	463-467	5	8
β-strand	476-480	5	8
β-strand	485-488	4	8
α-helix	490	1
β-strand	491	1	9
α-helix	492	1
α-helix	496-518	23
α-helix	524-533	10
α-helix	535-537	3
α-helix	547-551	5
α-helix	554-566	13
α-helix	579-588	10

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	3
β-strand	9-14	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	76	Homo sapiens	P62979 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 1	C	protein	250	Homo sapiens	P26358 (AlphaFold model)
Histone H3.1	D	protein	37	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5WVO_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 2 (C), FASTA

>5WVO_2 DNA (cytosine-5)-methyltransferase 1 (chains C)
PKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCF
SVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGFD
GGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLINK
IETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGV
TLGQRRAQAR

Sequence of entity 3 (D), FASTA

>5WVO_3 Histone H3.1 (chains D)
ARTKQTARKSTGGKAPRCQLATCAARKSAPATGGVKW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance. Ishiyama, S., Nishiyama, A., Saeki, Y. et al. Mol Cell (2017) 68:350-360.e7. DOI 10.1016/j.molcel.2017.09.037 · PubMed

Other PDB entries of the same protein (UniProt P62979 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NHE 1.26 Å, High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
7F0N 1.6 Å, Structure of deamidated Ubiquitin
8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
3NS8 1.71 Å, Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5
3N32 1.79 Å, The crystal structure of human Ubiquitin adduct with Zeise's salt
6SQS 1.83 Å, Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
3PHW 2.0 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.

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