8SVH: Ubiquitin variant i53 mutant L67R

Ubiquitin variant i53 mutant L67R bound to 53BP1 Tudor Domain. Determined by X-ray diffraction at 1.16 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 1.16 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,809
Mol. weight: 22.62 kDa
Released: 27 Mar 2024

Explore 8SVH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SVH contains 8 α-helices and 21 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1490-1493	4	1
β-strand	1501	1	2
β-strand	1502-1510	9	1
β-strand	1514-1519	6	1
β-strand	1524-1528	5	1
α-helix	1529-1531	3
β-strand	1532-1533	2	1
α-helix	1538-1539	2
β-strand	1543-1547	5	3
β-strand	1552-1564	13	3
β-strand	1567-1574	8	3
β-strand	1577-1582	6	3
α-helix	1583-1585	3
β-strand	1586-1587	2	3
β-strand	1588	1	2
α-helix	1590-1600	11
β-strand	1601	1	1

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	4
β-strand	12-17	6	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	68-69	2	3
β-strand	70-73	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor protein p53 binding protein 1	A	protein	124	Homo sapiens	Q12888 (AlphaFold model)
Ubiquitin variant i53: mutant L67R	B	protein	78	Homo sapiens	B4DV12 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SVH_1 Tumor protein p53 binding protein 1 (chains A)
GPGSNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIP
LDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQ
YGLG

Sequence of entity 2 (B), FASTA

>8SVH_2 Ubiquitin variant i53: mutant L67R (chains B)
GPGSMLIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLAFAGKSLEDGRTL
SDYNILKDSKRHPLLRLR

Primary citation

Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Perez-Bermejo, J.A., Efagene, O., Matern, W.M. et al. Nat Commun (2024) 15:2625-2625. DOI 10.1038/s41467-024-46816-5 · PubMed

Other PDB entries of the same protein (UniProt Q12888 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SVI 1.15 Å, Ubiquitin variant i53:Mutant L67H with 53BP1 Tudor domain
8SVG 1.21 Å, Ubiquitin variant i53 in complex with 53BP1 Tudor domain
2G3R 1.25 Å, Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution
6VA5 1.28 Å, Tudor Domain of Tumor suppressor p53BP1 with MFP-4184
6VIP 1.36 Å, Tudor domain of tumor suppressor P53BP1 with mfp-6008
7LIN 1.44 Å, X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
3LGF 1.5 Å, Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2
4RG2 1.5 Å, Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand
8SVJ 1.5 Å, Ubiquitin variant i53: mutant VHH with 53BP1 Tudor domain
8F0W 1.52 Å, Tudor Domain of Tumor suppressor p53BP1 with MFP-5956
3LGL 1.6 Å, Crystal structure of the 53BP1 tandem tudor domain in complex with p53K382me2
8SWJ 1.6 Å, Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531

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