4Z96: DNMT1

Crystal structure of DNMT1 in complex with USP7. Determined by X-ray diffraction at 2.85 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,119
Mol. weight: 65.35 kDa
Released: 12 Oct 2016

Explore 4Z96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z96 contains 26 α-helices and 36 β-strands across 1 chain. 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: 26 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	561-563	3
β-strand	564-571	8	1
α-helix	572-575	4
α-helix	589-591	3
β-strand	592-597	6	1
β-strand	601	1	2
α-helix	602-613	12
α-helix	617-619	3
β-strand	620-624	5	1
β-strand	625-627	3	3
β-strand	633-635	3	3
α-helix	643-645	3
β-strand	647	1	2
α-helix	648-652	5
β-strand	658-664	7	1
α-helix	667-671	5
α-helix	674-678	5
β-strand	684-693	10	4
α-helix	694-696	3
β-strand	698-708	11	4
β-strand	712	1	5
α-helix	713-716	4
α-helix	717-724	8
β-strand	732-739	8	4
β-strand	742-745	4	4
β-strand	752	1	5
α-helix	753-756	4
β-strand	765-770	6	4
α-helix	773-777	5
α-helix	783-792	10
β-strand	793-800	8	6
β-strand	809-814	6	6
β-strand	818	1	7
α-helix	819-828	10
α-helix	834-836	3
β-strand	837-840	4	6
β-strand	852	1	6
β-strand	860	1	7
α-helix	861-864	4
α-helix	873	1
β-strand	874-880	7	6
α-helix	885-888	4
β-strand	891	1	8
β-strand	894-899	6	9
β-strand	905-910	6	9
β-strand	913	1	8
β-strand	917	1	10
α-helix	918-926	9
β-strand	939-945	7	9
β-strand	948-952	5	9
β-strand	958	1	10
α-helix	959-961	3
β-strand	969-974	6	9
α-helix	975-976	2
α-helix	977-979	3
β-strand	989-995	7	11
β-strand	1002-1010	9	11
α-helix	1017-1028	12
β-strand	1039-1044	6	11
β-strand	1047-1051	5	11
α-helix	1074-1075	2
β-strand	1076-1080	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A	protein	530	Homo sapiens	Q93009 (AlphaFold model)
DNA (cytosine-5)-methyltransferase 1	C	protein	33	Homo sapiens	P26358 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4Z96_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A)
SGPLGSEAHLYMQVQIVAEDQFCGHQGNDMYDEEKVKYTVFKVLKNSSLAEFVQSLSQTM
GFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAASG
ATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLI
LYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHR
VDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYRDGPGNPL
RHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFREEEITLYPD
KHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIE
EIPLDQVDIDKENEMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQEK
EFEKFKFAIVMMGRHQYINEDEYEVNLKDFEPQPGNMSHPRPWLGLDHFN

Sequence of entity 2 (C), FASTA

>4Z96_2 DNA (cytosine-5)-methyltransferase 1 (chains C)
SDWPNHARSPGNKGKGKGKGKGKPKSQACEPSE

Primary citation

Crystal structure of DNMT1 in complex with USP7. Zhang, Z.M., Song, J. To be published.

Other PDB entries of the same protein (UniProt Q93009 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YSI 1.02 Å, Structure of USP7 with a novel viral protein
5KYC 1.43 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin…
5KYF 1.45 Å, Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin
2FOJ 1.6 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with p53 peptide…
2XXN 1.6 Å, Structure of the vIRF4-HAUSP TRAF domain complex
5KYD 1.62 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin
12ZJ 1.63 Å, Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
2F1W 1.65 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7
1YY6 1.7 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1…
2F1Y 1.7 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide
4KG9 1.7 Å, Crystal Structure Of USP7-NTD with MCM-BP
5N9T 1.73 Å, Crystal structure of USP7 in complex with a potent, selective and reversible…

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