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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MONOCYTE CHEMOATTRACTANT PROTEIN 4 (MCP-4/CCL13)
 
Authors :  J. Lubkowski, C. Barinka
Date :  14 Sep 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Biol. Unit 3:  A  (4x)
Biol. Unit 4:  B  (4x)
Keywords :  Ccl13, Mcp-4, Cc Chemokine Family, Chemotaxis, Monocytes, Cytokine, Inflammatory Response, Pyrrolidone Carboxylic Acid, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Barinka, A. Prahl, J. Lubkowski
Structure Of Human Monocyte Chemoattractant Protein 4 (Mcp-4/Ccl13).
Acta Crystallogr. , Sect. D V. 64 273 2008
PubMed-ID: 18323622  |  Reference-DOI: 10.1107/S0907444907066164

(-) Compounds

Molecule 1 - SMALL-INDUCIBLE CYTOKINE A13
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11D
    Expression System StrainBL21(DE3)TRXB
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCCL13, MCP4, NCC1, SCYA13
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCCL13, MONOCYTE CHEMOTACTIC PROTEIN 4, MCP-4, MONOCYTE CHEMOATTRACTANT PROTEIN 4, CK-BETA-10, NCC-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (4x)AB
Biological Unit 3 (4x)A 
Biological Unit 4 (4x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2TFA1Ligand/IonTRIFLUOROACETIC ACID
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2TFA1Ligand/IonTRIFLUOROACETIC ACID
Biological Unit 2 (2, 28)
No.NameCountTypeFull Name
1SO424Ligand/IonSULFATE ION
2TFA4Ligand/IonTRIFLUOROACETIC ACID
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2TFA-1Ligand/IonTRIFLUOROACETIC ACID
Biological Unit 4 (2, 16)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2TFA4Ligand/IonTRIFLUOROACETIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:18 , ILE A:20 , SER A:21 , ARG A:24 , THR A:32 , SER A:33 , HOH A:107BINDING SITE FOR RESIDUE SO4 A 76
2AC2SOFTWARESER A:9 , LYS A:18 , ARG A:24 , THR A:32 , ARG A:34 , LYS A:48 , HOH A:84 , HOH A:110 , LEU B:5BINDING SITE FOR RESIDUE SO4 A 77
3AC3SOFTWARELEU A:5 , SER B:9 , LYS B:18 , ARG B:24 , THR B:32 , ARG B:34 , LYS B:48 , HOH B:87 , HOH B:100BINDING SITE FOR RESIDUE SO4 B 76
4AC4SOFTWARELYS A:55 , LYS B:18 , SER B:21 , ARG B:24 , THR B:32 , SER B:33 , HOH B:99BINDING SITE FOR RESIDUE SO4 B 77
5AC5SOFTWARETHR A:10 , ARG A:24 , THR A:44 , LEU A:46 , LYS A:48 , HOH A:84 , HOH A:114 , HOH A:115BINDING SITE FOR RESIDUE SO4 A 78
6AC6SOFTWARELYS B:26BINDING SITE FOR RESIDUE SO4 B 78
7AC7SOFTWAREARG B:24 , THR B:44 , LYS B:45 , LEU B:46 , LYS B:48 , HOH B:97 , HOH B:101BINDING SITE FOR RESIDUE TFA B 79

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:11 -A:35
2A:12 -A:51
3B:11 -B:35
4B:12 -B:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RA4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048706N29SCCL13_HUMANPolymorphism34566308A/BN6S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048706N29SCCL13_HUMANPolymorphism34566308A/BN6S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048706N29SCCL13_HUMANPolymorphism34566308A/BN6S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048706N29SCCL13_HUMANPolymorphism34566308AN6S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048706N29SCCL13_HUMANPolymorphism34566308BN6S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL13_HUMAN34-75
 
  2A:11-52
B:11-52
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL13_HUMAN34-75
 
  2A:11-52
B:11-52
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL13_HUMAN34-75
 
  8A:11-52
B:11-52
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL13_HUMAN34-75
 
  4A:11-52
-
Biological Unit 4 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL13_HUMAN34-75
 
  4-
B:11-52

(-) Exons   (0, 0)

(no "Exon" information available for 2RA4)

(-) 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:65
 aligned with CCL13_HUMAN | Q99616 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:65
                                    35        45        55        65        75        85     
           CCL13_HUMAN   26 DALNVPSTCCFTFSSKKISLQRLKSYVITTSRCPQKAVIFRTKLGKEICADPKEKWVQNYMKHLG 90
               SCOP domains d2ra4a_ A: automated matches                                      SCOP domains
               CATH domains 2ra4A00 A:3-67  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---S------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CC  PDB: A:11-52          --------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  2ra4 A  3 DALNVPSTCCFTFSSKKISLQRLKSYVITTSRCPQKAVIFRTKLGKEICADPKEKWVQNYMKHLG 67
                                    12        22        32        42        52        62     

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with CCL13_HUMAN | Q99616 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:65
                                    35        45        55        65        75        85     
           CCL13_HUMAN   26 DALNVPSTCCFTFSSKKISLQRLKSYVITTSRCPQKAVIFRTKLGKEICADPKEKWVQNYMKHLG 90
               SCOP domains d2ra4b_ B: automated matches                                      SCOP domains
               CATH domains 2ra4B00 B:3-67  [code=2.40.50.40, no name defined]                CATH domains
           Pfam domains (1) IL8-2ra4B01 B:3-66                                              - Pfam domains (1)
           Pfam domains (2) IL8-2ra4B02 B:3-66                                              - Pfam domains (2)
         Sec.struct. author ......eee.........hhh.eeeeee.........eeeee....eeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---S------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CC  PDB: B:11-52          --------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  2ra4 B  3 DALNVPSTCCFTFSSKKISLQRLKSYVITTSRCPQKAVIFRTKLGKEICADPKEKWVQNYMKHLG 67
                                    12        22        32        42        52        62     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CCL13_HUMAN | Q99616)
molecular function
    GO:0048020    CCR chemokine receptor binding    Interacting selectively and non-covalently with a CCR 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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0071346    cellular response to interferon-gamma    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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
    GO:0071347    cellular response to interleukin-1    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 an interleukin-1 stimulus.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    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:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0048245    eosinophil chemotaxis    The movement of an eosinophil in response to an external stimulus.
    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:0048247    lymphocyte chemotaxis    The directed movement of a lymphocyte in response to an external stimulus.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    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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