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(-) Description

Title :  STRUCTURE OF A NANOBODY-BOUND 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 :  2.89
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gpcr, Chemokine, Membrane Protein, Complex, Viral Protein-Signalling Protein 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
    Mutation: YES
    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
 
Molecule 3 - NANOBODY 7
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1CLR2Ligand/IonCHOLESTEROL
2OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4SIN1Ligand/IonSUCCINIC ACID
5UNL7Ligand/IonUNKNOWN LIGAND

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:243 , LEU A:246 , CLR A:402binding site for residue CLR A 401
2AC2SOFTWAREPHE A:249 , LEU A:253 , SER A:268 , ARG A:271 , LEU A:279 , CLR A:401binding site for residue CLR A 402
3AC3SOFTWAREPRO A:34 , PHE A:38binding site for residue OLC A 403
4AC4SOFTWAREGLY A:224 , ARG A:228 , ILE A:231 , LEU A:235 , OLC A:406 , OLC A:407binding site for residue OLC A 404
5AC5SOFTWAREPHE A:46 , ILE A:49 , LEU A:289 , PHE A:293 , ARG A:299 , LEU A:302binding site for residue OLC A 405
6AC6SOFTWARETYR A:209 , ARG A:213 , ILE A:231 , VAL A:234 , OLC A:404binding site for residue OLC A 406
7AC7SOFTWARESER A:202 , TYR A:209 , ARG A:210 , ARG A:213 , ARG A:225 , ARG A:228 , OLC A:404 , OLC A:408binding site for residue OLC A 407
8AC8SOFTWARELEU A:289 , LEU A:290 , OLC A:407binding site for residue OLC A 408
9AC9SOFTWARELEU A:119 , THR A:123 , GLY A:195binding site for residue SIN A 416

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:263
2A:104 -A:173
3B:8 -B:34
4B:12 -B:50
5C:22 -C:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XT1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XT1)

(-) 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:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xt1 A  15 DYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNFLVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDSVPCTLLTACFYVAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQCMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIAVVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYVFVGTKFRQELHCLLAEFR 310
                                    24        34        44        54        64        74        84        94||     109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
                                                                                                           95|                                                                                                                                                                                                                 
                                                                                                           101                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee............eeeeee.hhhhh...eeeee....eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4xt1 B   1 xHHGVTKCAITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQ  68
                            |       10        20        30        40        50        60        
                            1-PCA                                                               


Chain C from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee.....eeeeeeee......eeeeeeeee.....eeeeeeee....eee.......eeeeee....eeeeeee..hhhhheeeeeeeee.......ee...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4xt1 C   1 QVQLVESGGGLVRPGGSLRLSCAASGSIFTIYAMGWYRQAPGKQRELVARITFGGDTNYADSVKGRFTISRDNAKNAVYLQMNSLKPEDTAVYYCNAEETIVEEADYWGQGTQVTV 116
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4XT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XT1)

(-) Gene Ontology  (67, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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: 4xt3
        X3CL1_HUMAN | P78423: 1b2t 1f2l 3ona 4xt3

(-) Related Entries Specified in the PDB File

4xt3