5WB2

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 

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Ligand Structure Quality Assessment 


This is version 2.0 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-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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope protein US28, nanobody 7 fusion proteinA460Human betaherpesvirus 5, Lama glama
This entity is chimeric		Mutation(s): 0 
Gene Names: US28
Membrane Entity: Yes 
UniProt
Find proteins for P69333 (Human cytomegalovirus (strain Towne))
Explore P69333 
Go to UniProtKB:  P69333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69333
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CX3CL1 proteinB76Homo sapiensMutation(s): 0 
Gene Names: CX3CL1, FKN, NTT, SCYD1, A-152E5.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78423 (Homo sapiens)
Explore P78423 
Go to UniProtKB:  P78423
PHAROS:  P78423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78423
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
nanobody B1C [auth D]131synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N		 Ligand Interaction
OLC
Query on OLC
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]		(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
K [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM		A L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
PCA
Query on PCA		C [auth D]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/582
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.17α = 90
b = 128.94β = 90
c = 127.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 2.0: 2020-01-01
    Changes: Author supporting evidence, Polymer sequence