4YSI | pdb_00004ysi

Structure of USP7 with a novel viral protein

• PDB DOI: https://doi.org/10.2210/pdb4YSI/pdb

• Classification: HYDROLASE/Peptide
• Organism(s): Homo sapiens, Human gammaherpesvirus 8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-17 Released: 2016-02-03 
• Deposition Author(s): Chavoshi, S., Saridakis, V.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structure of USP7 with a novel viral protein

Chavoshi, S., Egorova, O., Lacdao, I.K., Farhadi, S., Sheng, Y., Saridakis, V.

(2016) J Biological Chem 

• DOI: https://doi.org/10.1074/jbc.M115.710632

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.59 kDa 
• Atom Count: 1,466 
• Modeled Residue Count: 146 
• Deposited Residue Count: 151 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	A	143	Homo sapiens	Mutation(s): 0  Gene Names: USP7, HAUSP EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens) Explore Q93009  Go to UniProtKB:  Q93009
PHAROS:  Q93009 GTEx:  ENSG00000187555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-PRO-GLY-GLU-GLY-PRO-SER-GLY	B	8	Human gammaherpesvirus 8	Mutation(s): 0
UniProt
Find proteins for F5HF68 (Human herpesvirus 8 type P (isolate GK18)) Explore F5HF68  Go to UniProtKB:  F5HF68

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.975	α = 90
b = 69.975	β = 90
c = 45.444	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
RESOLVE	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Chavoshi, S., Saridakis, V.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	106583

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description