6VCS: SRA domain of UHRF1

SRA domain of UHRF1 in complex with DNA. Determined by X-ray diffraction at 1.7 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 5,084
Mol. weight: 78.95 kDa
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6VCS contains 22 α-helices and 30 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: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-421	2
β-strand	429-430	2	1
α-helix	433-438	6
β-strand	449-452	4	1
β-strand	456-462	7	1
β-strand	471	1	1
β-strand	475-479	5	1
α-helix	503-511	9
β-strand	522-523	2	1
α-helix	527-529	3
β-strand	533-538	6	1
α-helix	539-543	5
β-strand	553-568	16	1
β-strand	574-582	9	1
α-helix	587-588	2
α-helix	592-600	9
β-strand	606	1	1

Chain B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-421	2
β-strand	429-430	2	2
α-helix	433-438	6
β-strand	449-452	4	2
β-strand	456-462	7	2
β-strand	471	1	2
β-strand	475-479	5	2
α-helix	503-511	9
β-strand	522-523	2	2
α-helix	527-529	3
β-strand	533-538	6	2
α-helix	539-544	6
β-strand	553-568	16	2
β-strand	574-582	9	2
α-helix	587-588	2
α-helix	592-600	9
β-strand	606	1	2
α-helix	611-614	4

Chain E: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-421	2
β-strand	429-430	2	3
α-helix	433-439	7
β-strand	449-452	4	3
β-strand	456-462	7	3
β-strand	471	1	3
β-strand	475-479	5	3
α-helix	503-510	8
β-strand	522-523	2	3
α-helix	527-529	3
β-strand	533-538	6	3
α-helix	539-542	4
β-strand	553-568	16	3
β-strand	574-582	9	3
α-helix	587-588	2
α-helix	592-601	10
β-strand	605-606	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A, B, E	protein	211	Homo sapiens	Q96T88 (AlphaFold model)
DNA (5'-d(gpcpcptpgptpapcpapgpgpc)-3')	C, D	DNA	12	synthetic construct
Unk-unk-unk-unk	G	protein	6	Homo sapiens

Sequence of entity 1 (A, B, E), FASTA

>6VCS_1 E3 ubiquitin-protein ligase UHRF1 (chains A, B, E)
MPSNHYGPIPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDH
GNFFTYTGSGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKP
VRVVRNVKGGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTK
EGKDRIKKLGLTMQYPEGYLEALANHHHHHH

Sequence of entity 2 (C, D), FASTA

>6VCS_2 DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3') (chains C, D)
GCCTGTACAGGC

Sequence of entity 3 (G), FASTA

>6VCS_3 UNK-UNK-UNK-UNK (chains G)
XXXXXX

Primary citation

SRA domain of UHRF1 in complex with DNA. Dong, C., Tempel, W., Bountra, C. et al. To be published.

Other PDB entries of the same protein (UniProt Q96T88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W92 1.3 Å, Human UHRF1 TTD domain
6VYJ 1.39 Å, Human UHRF1 TTD domain in complex with a fragment
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
3ZVZ 1.45 Å, PHD finger of human UHRF1
7FB7 1.45 Å, Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
8XV6 1.6 Å, Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
6B9M 1.68 Å, Crystal structure of UHRF1 TTD domain in complex with the polybasic region
6IIW 1.7 Å, Crystal structure of human UHRF1 PHD finger in complex with PAF15
3BI7 1.7 Å, Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1
5YYA 1.7 Å, Crystal structure of Tandem Tudor Domain of human UHRF1
3FL2 1.75 Å, Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1
3SHB 1.8 Å, Crystal Structure of PHD Domain of UHRF1

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