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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE IP-10
 
Authors :  T. Jabeen, P. Leonard, H. Jamaluddin, K. R. Acharya
Date :  30 Aug 07  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ip-10/Cxcl10, Chemokine, Chemotaxis, Inflammatory Response, Attractant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Jabeen, P. Leonard, H. Jamaluddin, K. R. Acharya
Structure Of Mouse Ip-10, A Chemokine
Acta Crystallogr. , Sect. D V. 64 611 2008
PubMed-ID: 18560148  |  Reference-DOI: 10.1107/S0907444908007026
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMALL-INDUCIBLE CYTOKINE B10
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 23-89
    Gene: CXCL10, CRG2, IFI10, INP10, SCYB10
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CXCL-10 CHEMOKINE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R3Z)

(-) Sites  (0, 0)

(no "Site" information available for 2R3Z)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:36
2A:11 -A:53
3B:9 -B:36
4B:11 -B:53
5C:9 -C:36
6C:11 -C:53
7D:9 -D:36
8D:11 -D:53

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R3Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R3Z)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.CXL10_MOUSE30-76
 
 
 		  4A:9-55
B:9-55
C:9-55
D:9-55

(-) Exons   (2, 8)

Asymmetric/Biological Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENSMUST000000388161bENSMUSE00000881021chr5:92777908-92777780129CXL10_MOUSE1-21210--
1.2aENSMUST000000388162aENSMUSE00000321820chr5:92777241-92777115127CXL10_MOUSE21-63434A:1-42
B:1-42
C:4-42
D:4-42		42
42
39
39
1.3aENSMUST000000388163aENSMUSE00000402325chr5:92776920-9277683190CXL10_MOUSE63-93314A:42-68
B:42-67
C:42-68
D:42-67		27
26
27
26
1.4ENSMUST000000388164ENSMUSE00000694207chr5:92776411-92775664748CXL10_MOUSE93-9860--

(-) 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:68
 aligned with CXL10_MOUSE | P17515 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:68
                                    31        41        51        61        71        81        
           CXL10_MOUSE   22 IPLARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKAF 89
               SCOP domains d2r3za_ A: automated matches                                         SCOP domains
               CATH domains 2r3zA00 A:1-68  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee................eeeee.........eeeee......eeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CXC  PDB: A:9-55 UniProt: 30-76------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-42 UniProt: 21-63     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3a  PDB: A:42-68     Transcript 1 (2)
                  2r3z A  1 IPLARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKAF 68
                                    10        20        30        40        50        60        


Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CXL10_MOUSE | P17515 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:67
                                    31        41        51        61        71        81       
           CXL10_MOUSE   22 IPLARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKA 88
               SCOP domains d2r3zb_ B: automated matches                                        SCOP domains
               CATH domains 2r3zB00 B:1-67  [code=2.40.50.40, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..............eeeeeee.........eeeeee....eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CXC  PDB: B:9-55 UniProt: 30-76------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-42 UniProt: 21-63     ------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3a  PDB: B:42-67    Transcript 1 (2)
                  2r3z B  1 IPLARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKA 67
                                    10        20        30        40        50        60       


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with CXL10_MOUSE | P17515 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:65
                                    34        44        54        64        74        84     
           CXL10_MOUSE   25 ARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKAF 89
               SCOP domains d2r3zc_ C: automated matches                                      SCOP domains
               CATH domains 2r3zC00 C:4-68  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....hhh.eeeeeee.........eeeeee.....eeee...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SMALL_CYTOKINES_CXC  PDB: C:9-55 UniProt: 30-76------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:4-42 UniProt: 21-63  -------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3a  PDB: C:42-68     Transcript 1 (2)
                  2r3z C  4 ARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKAF 68
                                    13        23        33        43        53        63     


Chain D from PDB  Type:PROTEIN  Length:64
 aligned with CXL10_MOUSE | P17515 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:64
                                    34        44        54        64        74        84    
           CXL10_MOUSE   25 ARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKA 88
               SCOP domains d2r3zd_ D: automated matches                                     SCOP domains
               CATH domains 2r3zD00 D:4-67  [code=2.40.50.40, no name defined]               CATH domains
           Pfam domains (1) IL8-2r3zD01 D:4-67                                               Pfam domains (1)
           Pfam domains (2) IL8-2r3zD02 D:4-67                                               Pfam domains (2)
           Pfam domains (3) IL8-2r3zD03 D:4-67                                               Pfam domains (3)
           Pfam domains (4) IL8-2r3zD04 D:4-67                                               Pfam domains (4)
         Sec.struct. author ..........ee....hhh.eeeeeee.........eeeeee.hhh.eeee...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SMALL_CYTOKINES_CXC  PDB: D:9-55 UniProt: 30-76------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: D:4-42 UniProt: 21-63  ------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3a  PDB: D:42-67    Transcript 1 (2)
                  2r3z D  4 ARTVRCNCIHIDDGPVRMRAIGKLEIIPASLSCPRVEIIATMKKNDEQRCLNPESKTIKNLMKA 67
                                    13        23        33        43        53        63
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CXL10_MOUSE | P17515)
molecular function
    GO:0045236    CXCR chemokine receptor binding    Interacting selectively and non-covalently with a chemokine receptor in the CXCR family.
    GO:0048248    CXCR3 chemokine receptor binding    Interacting selectively and non-covalently with a the CXCR3 chemokine receptor.
    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.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0010818    T cell chemotaxis    The directed movement of a T cell in response to an external stimulus. A T cell is a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
    GO:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a 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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0042118    endothelial cell activation    The change in morphology and behavior of an endothelial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0045662    negative regulation of myoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:1901740    negative regulation of myoblast fusion    Any process that stops, prevents or reduces the frequency, rate or extent of myoblast fusion.
    GO:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0030816    positive regulation of cAMP metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0043950    positive regulation of cAMP-mediated signaling    Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0010819    regulation of T cell chemotaxis    Any process that modulates the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:1901509    regulation of endothelial tube morphogenesis    Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.
    GO:0010996    response to auditory stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an auditory stimulus.
    GO:0009409    response to cold    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0033280    response to vitamin D    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  CXL10_MOUSE | P17515
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(-) Related Entries Specified in the PDB File

1o7y CRYSTAL STRUCTURE OF IP-10 M-FORM
1o7z CRYSTAL STRUCTURE OF IP-10 T-FORM
1o80 CRYSTAL STRUCTURE OF IP-10 H-FORM