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(-) Description

Title :  CRYSTAL STRUCTURE OF VIRAL CHEMOKINE BINDING PROTEIN R17 IN COMPLEX WITH CCL3
 
Authors :  O. Y. Lubman, D. H. Fremont
Date :  01 May 15  (Deposition) - 18 Nov 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,F,L
Biol. Unit 1:  B,F  (1x)
Biol. Unit 2:  A,L  (1x)
Keywords :  Rhvp Chemokine Binding Protein In Complex With Chemokine Ccl3, Chemokine Binding Protein-Chemokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Y. Lubman, D. H. Fremont
Parallel Evolution Of Chemokine Binding By Structurally Related Herpesvirus Decoy Receptors.
Structure V. 24 57 2016
PubMed-ID: 26671708  |  Reference-DOI: 10.1016/J.STR.2015.10.018

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: B, A
    Engineered: YES
    Expression System: MAMMALIAN EXPRESSION VECTOR PBGSA
    Expression System Cell: ENDOTHELIAL
    Expression System Cell Line: 293F
    Expression System Taxid: 285261
    Gene: RHVP-L.R17, RHVP.R17
    Mutation: YES
    Organism Scientific: CRICETID HERPESVIRUS 2
    Organism Taxid: 1605972
 
Molecule 2 - C-C MOTIF CHEMOKINE 3
    Chains: F, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CCL3, MIP1A, SCYA3
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HEPARIN-BINDING CHEMOTAXIS PROTEIN,L2G25B,MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA,MIP-1-ALPHA,SIS-ALPHA,SMALL-INDUCIBLE CYTOKINE A3,TY-5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFL
Biological Unit 1 (1x):  BF 
Biological Unit 2 (1x): A  L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:158 , LEU A:159 , ASN A:183binding site for residue NAG A 501
2AC2SOFTWAREGLU A:204 , ASN A:205binding site for Mono-Saccharide NAG A 502 bound to ASN A 205
3AC3SOFTWAREALA B:101 , ASN B:103binding site for Mono-Saccharide NAG B 502 bound to ASN B 103
4AC4SOFTWAREASN B:205binding site for Mono-Saccharide NAG B 501 bound to ASN B 205

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:52 -A:177
2A:81 -A:84
3A:96 -A:160
4A:197 -A:208
5A:223 -A:278
6A:326 -A:347
7B:52 -B:177
8B:81 -B:84
9B:96 -B:160
10B:197 -B:208
11B:223 -B:278
12B:326 -B:347
13F:11 -F:34
14F:12 -F:50
15L:11 -L:34
16L:12 -L:50

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu B:38 -Pro B:39
2Leu A:38 -Pro A:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZLT)

(-) Sequences/Alignments

Asymmetric 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee................hhhhhhhhhh.eeeeee...eee..eeeeeee..........eeeeeeeeee........hhhhheee.........eeeeee......eeeeeeeeeeee...eeeeee...hhhh.eeeeeeeee.....eeeeeee....hhh.eeeeee........eeeeeeeeeeee..eeeeee..eeeeee..eeeeeeeeeee......eeeeeee...hhhhhhhh........ee...eeeeeee.hhhhhh....eeeeeee.........eeeeeee...................eeeeee....eeeeeeeee........eeeeeeee...eeeeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zlt A  18 SSRLLTQDILFRKDRQATISLPIKLPVEDIITQTCDKITYGPLKFLDLLEKETAVLPLSTDITCPACLGRAVLVGKWECPAHVAVNESDLTVFGPNKEEHVPQFVTVQQPSDGKMQRLFFAKFLGTEESLAVLRVPGPDGHLCIQEALIHFKELSGAGVCSLWKANDSREEGLEMKQVDCLETTVLENQTCIATTLSKKIYHRLYCGERLMTGGQVSTRVLLTALGFYKVPKGMVYVHLIDSGSEDYMEYSECEEVTPGRYEDKQISYTFYTDLFQTADGEPVLASVWGTSGLKDSAYESCAFVIPTDGEEDLVPRRIMSKCYPFRLTYHPSTMTVRLDVRVEKHHGATDQGFVFLKMESGTYSEGREYYLDRVLW 401
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395      
                                                                                                                                                                                                                                                              246|                                                                                                                                                  
                                                                                                                                                                                                                                                               255                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee................hhhhhhhhhh.eeeeee...eee..eeeeeee..........eeeeeeeeee........hhhhheee.........eeeeeee....eeeeeeeeeeeee...eeeeee...hhhh.eeeeeeeee.....eeeeeee........eeeeee........eeeeeeeeeeee..eeeeee..eeeeee..eeeeeeeeeee..........eeeeeee.....hhhhhh.......ee...eeeeeee.hhhhhh....eeeeeeee........eeeeeee..........ee.......eeeeee....eeeeeee..........eeeeeeee...eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zlt B  18 SSRLLTQDILFRKDRQATISLPIKLPVEDIITQTCDKITYGPLKFLDLLEKETAVLPLSTDITCPACLGRAVLVGKWECPAHVAVNESDLTVFGPNKEEHVPQFVTVQQPSDGKMQRLFFAKFLGTEESLAVLRVPGPDGHLCIQEALIHFKELSGAGVCSLWKANDSREEGLEMKQVDCLETTVLENQTCIATTLSKKIYHRLYCGERLMTGGQVSTRVLLTALGFYKRQPVPKGMVYVHLIDSGSEDYMEYSECEEVTPGRYEDKQISYTFYTDLFQTADGEPVLASVWGTSGLKDSAYESCAFVIPTDGEEDLVPRRIMSKCYPFRLTYHPSTMTVRLDVRVEKHHGATDQGFVFLKMESGTYSEGREYYLDRVLW 401
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247 ||    262       272       282       292       302       312       322       332       342       352       362       372       382       392         
                                                                                                                                                                                                                                                                 249|                                                                                                                                                  
                                                                                                                                                                                                                                                                  255                                                                                                                                                  


Chain F from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....hhh.eeeeee........eeeeee....eeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 4zlt F   7 TPTACCFSYSRKIPRQFIVAYFETSSLCSQPGVIFLTKRNRQICADSKETWVQEYITDLELN  68
                                    16        26        36        46        56        66  


Chain L from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhh.eeeeee........eeeeee....eeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 4zlt L   7 TPTACCFSYSRKIPRQFIVAYFETSSLCSQPGVIFLTKRNRQICADSKETWVQEYITDLELN  68
                                    16        26        36        46        56        66
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4ZLT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (70, 70)

Asymmetric Unit(hide GO term definitions)

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  E9M5R0_9GAMA | E9M5R0
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 Related Entries

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

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        E9M5R0_9GAMA | E9M5R0: 4zkq

(-) Related Entries Specified in the PDB File

2x6g HUMAN CHEMOKINE CCL3
4zkq 4ZKQ CONTAINS THE SAME PROTEIN WITHOUT CHEMOKINE CCL3