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(-) Description

Title :  CRYSTAL STRUCTURE OF A VIRAL CHEMOKINE
 
Authors :  J. G. Luz, M. Yu, Y. Su, Z. Wu, Z. Zhou, R. Sun, I. A. Wilson
Date :  08 Jun 05  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Chemokine Fold, Greek Key Motif, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Luz, M. Yu, Y. Su, Z. Wu, Z. Zhou, R. Sun, I. A. Wilson
Crystal Structure Of Viral Macrophage Inflammatory Protein Encoded By Kaposi'S Sarcoma-Associated Herpesvirus At 1. 7A.
J. Mol. Biol. V. 352 1019 2005
PubMed-ID: 16140327  |  Reference-DOI: 10.1016/J.JMB.2005.08.011

(-) Compounds

Molecule 1 - FUNCTIONAL MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA HOMOLOG
    Chains: A, B, C, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector: PBLUEBAC2
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 8
    Organism Taxid: 37296
    Synonym: ORF K6, VMIP-I

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ZXT)

(-) Sites  (0, 0)

(no "Site" information available for 1ZXT)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:12 -A:36
2A:13 -A:52
3B:12 -B:36
4B:13 -B:52
5C:12 -C:36
6C:13 -C:52
7D:12 -D:36
8D:13 -D:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZXT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZXT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZXT)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZXT)

(-) 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:69
 aligned with Q76RJ0_HHV8 | Q76RJ0 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q76RJ0_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxta_ A: automated matches                                          SCOP domains
               CATH domains -----1zxtA01 A:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt A  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain A from PDB  Type:PROTEIN  Length:69
 aligned with Q98158_HHV8 | Q98158 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q98158_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxta_ A: automated matches                                          SCOP domains
               CATH domains -----1zxtA01 A:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt A  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with Q76RJ0_HHV8 | Q76RJ0 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q76RJ0_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtb_ B: automated matches                                          SCOP domains
               CATH domains -----1zxtB01 B:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt B  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with Q98158_HHV8 | Q98158 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q98158_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtb_ B: automated matches                                          SCOP domains
               CATH domains -----1zxtB01 B:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt B  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with Q76RJ0_HHV8 | Q76RJ0 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q76RJ0_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtc_ C: automated matches                                          SCOP domains
               CATH domains -----1zxtC01 C:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt C  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with Q98158_HHV8 | Q98158 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q98158_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtc_ C: automated matches                                          SCOP domains
               CATH domains -----1zxtC01 C:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt C  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with Q76RJ0_HHV8 | Q76RJ0 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q76RJ0_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtd_ D: automated matches                                          SCOP domains
               CATH domains -----1zxtD01 D:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
           Pfam domains (1) IL8-1zxtD01 D:5-67                                             ------ Pfam domains (1)
           Pfam domains (2) IL8-1zxtD02 D:5-67                                             ------ Pfam domains (2)
           Pfam domains (3) IL8-1zxtD03 D:5-67                                             ------ Pfam domains (3)
           Pfam domains (4) IL8-1zxtD04 D:5-67                                             ------ Pfam domains (4)
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt D  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with Q98158_HHV8 | Q98158 from UniProtKB/TrEMBL  Length:95

    Alignment length:69
                                                                                             95  
                                    38        48        58        68        78        88      |  
           Q98158_HHV8   29 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIA--  -
               SCOP domains d1zxtd_ D: automated matches                                          SCOP domains
               CATH domains -----1zxtD01 D:10-70  [code=2.40.50.40, no name defined]          --- CATH domains
           Pfam domains (1) IL8-1zxtD01 D:5-67                                             ------ Pfam domains (1)
           Pfam domains (2) IL8-1zxtD02 D:5-67                                             ------ Pfam domains (2)
           Pfam domains (3) IL8-1zxtD03 D:5-67                                             ------ Pfam domains (3)
           Pfam domains (4) IL8-1zxtD04 D:5-67                                             ------ Pfam domains (4)
         Sec.struct. author .....eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  1zxt D  5 VSYTPNSCCYGFQQHPPPVQILKEWYPTSPACPKPGVILLTKRGRQICADPSKNWVRQLMQRLPAIAHH 73
                                    14        24        34        44        54        64
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: IL8] (55)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q76RJ0_HHV8 | Q76RJ0)
molecular function
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
biological process
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A,B,C,D   (Q98158_HHV8 | Q98158)
molecular function
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
biological process
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1zxt
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  Q76RJ0_HHV8 | Q76RJ0
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  Q98158_HHV8 | Q98158
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 Related Entries

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

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