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(-) Description

Title :  STRUCTURE OF A VIRAL GPCR BOUND TO HUMAN CHEMOKINE CX3CL1
 
Authors :  J. S. Burg, K. M. Jude, D. Waghray, K. C. Garcia
Date :  22 Jan 15  (Deposition) - 04 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gpcr, Chemokine, Membrane Protein, Complex, Viral Protein-Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Burg, J. R. Ingram, A. J. Venkatakrishnan, K. M. Jude, A. Dukkipati, E. N. Feinberg, A. Angelini, D. Waghray, R. O. Dror, H. L. Ploegh, K. C. Garcia
Structural Biology. Structural Basis For Chemokine Recognition And Activation Of A Viral G Protein-Coupled Receptor.
Science V. 347 1113 2015
PubMed-ID: 25745166  |  Reference-DOI: 10.1126/SCIENCE.AAA5026

(-) Compounds

Molecule 1 - G-PROTEIN COUPLED RECEPTOR HOMOLOG US28
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S GNTI-
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: CYTOMEGALOVIRUS
    Organism Taxid: 10358
    Synonym: HHRF3
 
Molecule 2 - FRACTALKINE
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S GNTI-
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 25-101
    Gene: CX3CL1, FKN, NTT, SCYD1, A-152E5.2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: C-X3-C MOTIF CHEMOKINE 1,CX3C MEMBRANE-ANCHORED CHEMOKINE, NEUROTACTIN,SMALL-INDUCIBLE CYTOKINE D1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3PO41Ligand/IonPHOSPHATE ION
4UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:228binding site for residue PO4 A 402
2AC2SOFTWAREASN B:9 , ILE B:10 , GLN B:28 , GLN B:31binding site for Poly-Saccharide residues NAG B 101 through NAG B 103 bound to ASN B 9

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:263
2A:104 -A:173
3B:8 -B:34
4B:12 -B:50

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile B:19 -Pro B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XT3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XT3)

(-) Exons   (0, 0)

(no "Exon" information available for 4XT3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xt3 A  18 EDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNFLVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHASVPCTLLTACFYVAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQCMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIAVVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYVFVGTKFRQELHCLLAE 308
                                    27        37        47        57        67        77        87       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                         96|                                                                                                                                                                                                                
                                                                                                         100                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee............eeeeee.hhhhh...eeeee....eeee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4xt3 B   1 xHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQA  69
                            |       10        20        30        40        50        60         
                            1-PCA
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XT3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XT3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XT3)

(-) Gene Ontology  (67, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xt3
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  US28_HCMVA | P69332
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  X3CL1_HUMAN | P78423
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        US28_HCMVA | P69332: 4xt1
        X3CL1_HUMAN | P78423: 1b2t 1f2l 3ona 4xt1

(-) Related Entries Specified in the PDB File

4xt1