5WB1

Ligand-free US28 with stabilizing intracellular nanobody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy.

Miles, T.F., Spiess, K., Jude, K.M., Tsutsumi, N., Burg, J.S., Ingram, J.R., Waghray, D., Hjorto, G.M., Larsen, O., Ploegh, H.L., Rosenkilde, M.M., Garcia, K.C.

(2018) Elife 7

  • DOI: 10.7554/eLife.35850
  • Primary Citation of Related Structures:  
    5WB1, 5WB2

  • PubMed Abstract: 

    • Human cytomegalovirus has hijacked and evolved a human G-protein-coupled receptor into US28, which functions as a promiscuous chemokine 'sink' to facilitate evasion of host immune responses. To probe the molecular basis of US28's unique ligand cross- ...

    Human cytomegalovirus has hijacked and evolved a human G-protein-coupled receptor into US28, which functions as a promiscuous chemokine 'sink' to facilitate evasion of host immune responses. To probe the molecular basis of US28's unique ligand cross-reactivity, we deep-sequenced CX3CL1 chemokine libraries selected on 'molecular casts' of the US28 active-state and find that US28 can engage thousands of distinct chemokine sequences, many of which elicit diverse signaling outcomes. The structure of a G-protein-biased CX3CL1-variant in complex with US28 revealed an entirely unique chemokine amino terminal peptide conformation and remodeled constellation of receptor-ligand interactions. Receptor signaling, however, is remarkably robust to mutational disruption of these interactions. Thus, US28 accommodates and functionally discriminates amongst highly degenerate chemokine sequences by sensing the steric bulk of the ligands, which distort both receptor extracellular loops and the walls of the ligand binding pocket to varying degrees, rather than requiring sequence-specific bonding chemistries for recognition and signaling.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope protein US28, nanobody 7 fusion proteinA458Human betaherpesvirus 5, Lama glama
This entity is chimeric		Mutation(s): 0 
Gene Names: US28
Find proteins for P69333 (Human cytomegalovirus (strain Towne))
Explore P69333 
Go to UniProtKB:  P69333
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/581 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.6α = 90
b = 38.3β = 107.4
c = 99.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097015

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence