7S6O | pdb_00007s6o

The crystal structure of Lys48-linked di-ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb7S6O/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2021-09-14 Released: 2021-09-22 
• Deposition Author(s): Osipiuk, J., Tesar, C., Lanham, B.T., Wydorski, P., Fushman, D., Joachimiak, L., Joachimiak, A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.

Wydorski, P.M., Osipiuk, J., Lanham, B.T., Tesar, C., Endres, M., Engle, E., Jedrzejczak, R., Mullapudi, V., Michalska, K., Fidelis, K., Fushman, D., Joachimiak, A., Joachimiak, L.A.

(2023) Nat Commun 14: 2366-2366

• PubMed: 37185902 
• DOI: https://doi.org/10.1038/s41467-023-38031-5
• Primary Citation Related Structures: 
  7RBR, 7RBS, 7S6O, 7S6P, 7UV5


• PubMed Abstract: 
  

  The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub ₂ ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub ₂ combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub ₂ are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub ₂ modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

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Organizational Affiliation: 
• Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616, USA.
Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA. [e-mail].
Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA. [e-mail].
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA. [e-mail].
Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. [e-mail].
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.41 kDa 
• Atom Count: 1,432 
• Modeled Residue Count: 148 
• Deposited Residue Count: 153 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	77	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth B], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37S6O

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.804	α = 90
b = 56.577	β = 93.37
c = 46.201	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Osipiuk, J., Tesar, C., Lanham, B.T., Wydorski, P., Fushman, D., Joachimiak, L., Joachimiak, A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2021-12-15
  Changes: Author supporting evidence, Structure summary
• Version 2.0: 2022-03-16
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-05-31
  Changes: Database references
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description