4XT1 | pdb_00004xt1

Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1

• PDB DOI: https://doi.org/10.2210/pdb4XT1/pdb

• Classification: VIRAL PROTEIN/SIGNALLING PROTEIN
• Organism(s): Cytomegalovirus, Homo sapiens, Vicugna pacos
• Expression System: Homo sapiens, Escherichia coli BL21
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-01-22 Released: 2015-03-04 
• Deposition Author(s): Burg, J.S., Jude, K.M., Waghray, D., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Models: experimental

Literature

Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.

Burg, J.S., Ingram, J.R., Venkatakrishnan, A.J., Jude, K.M., Dukkipati, A., Feinberg, E.N., Angelini, A., Waghray, D., Dror, R.O., Ploegh, H.L., Garcia, K.C.

(2015) Science 347: 1113-1117

• PubMed: 25745166 
• DOI: https://doi.org/10.1126/science.aaa5026
• Primary Citation Related Structures: 
  4XT1, 4XT3


• PubMed Abstract: 
  

  Chemokines are small proteins that function as immune modulators through activation of chemokine G protein-coupled receptors (GPCRs). Several viruses also encode chemokines and chemokine receptors to subvert the host immune response. How protein ligands activate GPCRs remains unknown. We report the crystal structure at 2.9 angstrom resolution of the human cytomegalovirus GPCR US28 in complex with the chemokine domain of human CX3CL1 (fractalkine). The globular body of CX3CL1 is perched on top of the US28 extracellular vestibule, whereas its amino terminus projects into the central core of US28. The transmembrane helices of US28 adopt an active-state-like conformation. Atomic-level simulations suggest that the agonist-independent activity of US28 may be due to an amino acid network evolved in the viral GPCR to destabilize the receptor's inactive state.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Computer Science, Stanford University, Stanford, CA 94305, USA. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.67 kDa 
• Atom Count: 3,978 
• Modeled Residue Count: 475 
• Deposited Residue Count: 587 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor homolog US28	A	362	Cytomegalovirus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P69332 (Human cytomegalovirus (strain AD169)) Explore P69332  Go to UniProtKB:  P69332

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fractalkine	B	91	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000006210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody 7	C	134	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth A], E [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
SIN	S [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
UNL	L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	Unknown ligand KDYFGRWQOYBRFD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/339

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.024	α = 90
b = 81.024	β = 90
c = 231.303	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Burg, J.S., Jude, K.M., Waghray, D., Garcia, K.C.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 2.0: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy
• Version 2.1: 2024-11-20
  Changes: Structure summary