4YSI: USP7 with a novel viral protein

Structure of USP7 with a novel viral protein. Determined by X-ray diffraction at 1.02 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 1.02 Å
Organisms: Homo sapiens, Human herpesvirus 8
Chains: 2
Atoms: 1,466
Mol. weight: 17.59 kDa
Released: 3 Feb 2016

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

Secondary structure: helices and β-sheets

4YSI contains 5 α-helices and 14 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: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	68-75	8	1
α-helix	78-80	3
β-strand	85-86	2	2
α-helix	87-89	3
β-strand	90-92	3	2
β-strand	95-105	11	2
β-strand	113-121	9	2
β-strand	131-140	10	1
α-helix	146-148	3
β-strand	150-159	10	1
β-strand	162	1	1
β-strand	164-172	9	2
α-helix	173-176	4
β-strand	185	1	3
β-strand	188	1	3
β-strand	189-197	9	1
α-helix	198-200	3
β-strand	201	1	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	47-48	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A	protein	143	Homo sapiens	Q93009 (AlphaFold model)
Ser-pro-gly-glu-gly-pro-ser-gly	B	protein	8	Human herpesvirus 8	F5HF68 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YSI_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A)
TSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCN
AESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKG
FIDDDKVTFEVFVQADAPHGVAW

Sequence of entity 2 (B), FASTA

>4YSI_2 SER-PRO-GLY-GLU-GLY-PRO-SER-GLY (chains B)
SPGEGPSG

Primary citation

Structure of USP7 with a novel viral protein. Chavoshi, S., Egorova, O., Lacdao, I.K. et al. J Biol Chem (2016). DOI 10.1074/jbc.M115.710632

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

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…
9DEM 1.77 Å, USP7 in complex with macrocycle MC04

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