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(-) Description

Title :  STRUCTURE OF HUMAN MIP-3A CHEMOKINE
 
Authors :  Z. A. Malik, B. F. Tack
Date :  16 Jun 06  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Macrophage Inflammatory Protein-3A, Dimer, Space Group I4, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. A. Malik, B. F. Tack
Structure Of Human Mip-3Alpha Chemokine.
Acta Crystallogr. , Sect. F V. 62 631 2006
PubMed-ID: 16820679  |  Reference-DOI: 10.1107/S1744309106006890
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMALL INDUCIBLE CYTOKINE A20
    ChainsA, B
    EngineeredYES
    Other DetailsTHE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymCCL20, MACROPHAGE INFLAMMATORY PROTEIN 3 ALPHA, MIP-3-ALPHA, LIVER AND ACTIVATION-REGULATED CHEMOKINE, CC CHEMOKINE LARC, BETA CHEMOKINE EXODUS-1, MIP-3A
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
2SO34Ligand/IonSULFITE ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:53 , THR A:54 , TRP A:55 , HIS B:16BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG A:25 , GLN A:26 , LEU A:27 , GLU A:30 , CYS A:32 , HOH A:307 , HOH A:369BINDING SITE FOR RESIDUE SO3 A 302
3AC3SOFTWAREARG A:13 , LEU A:15 , TRP A:55BINDING SITE FOR RESIDUE SO3 A 303
4AC4SOFTWAREALA A:28 , GLY A:31 , CYS A:32 , ASP A:33 , HOH A:308 , HOH A:322BINDING SITE FOR RESIDUE SO3 A 304
5AC5SOFTWARELEU A:27 , ILE A:37 , PRO A:51 , LYS B:66 , VAL B:67 , HOH B:207BINDING SITE FOR RESIDUE SO3 A 305
6AC6SOFTWARELYS A:66 , VAL A:67 , ASN A:69 , LYS B:52 , LYS B:57BINDING SITE FOR RESIDUE PEG A 201
7AC7SOFTWARELYS A:66 , GLN B:53 , THR B:54 , TRP B:55BINDING SITE FOR RESIDUE PEG B 202
8AC8SOFTWAREASP B:5 , HIS B:16 , LYS B:18 , PHE B:19 , LYS B:42BINDING SITE FOR RESIDUE PEG B 203
9AC9SOFTWAREHOH A:350 , HOH A:368 , HOH A:371 , ARG B:13 , HOH B:252BINDING SITE FOR RESIDUE PEG A 204

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:32
2A:7 -A:48
3B:6 -B:32
4B:7 -B:48

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011915V47MCCL20_HUMANPolymorphism1049617A/BV21M

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CCPS00472 Small cytokines (intercrine/chemokine) C-C subfamily signature.CCL20_HUMAN32-75
 
  2A:6-49
B:6-49

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003588131cENSE00001818481chr2:228678570-228678703134CCL20_HUMAN1-26260--
1.2bENST000003588132bENSE00000786519chr2:228680170-228680284115CCL20_HUMAN26-64392A:2-38
B:5-38
37
34
1.3ENST000003588133ENSE00000843780chr2:228681023-22868110078CCL20_HUMAN64-90272A:38-64
B:38-64
27
27
1.4bENST000003588134bENSE00001920600chr2:228681778-228682250473CCL20_HUMAN90-9672A:64-69
B:64-69
6
6

(-) 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 CCL20_HUMAN | P78556 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:68
                                    37        47        57        67        77        87        
           CCL20_HUMAN   28 SNFDCCLGYTDRILHPKFIVGFTRQLANEGCDINAIIFHTKKKLSVCANPKQTWVKYIVRLLSKKVKN 95
               SCOP domains ---d2hcia1 A:5-65 Macrophage inflammatory protein, MIP          ---- SCOP domains
               CATH domains 2hciA00 A:2-69  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhh.eeeeeeehhhhh....eeeeee.....eee.................... Sec.struct. author
                 SAPs(SNPs) -------------------M------------------------------------------------ SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CC  PDB: A:6-49             -------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:2-38 UniProt: 26-64-------------------------1.4b   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: A:38-64     ----- Transcript 1 (2)
                  2hci A  2 SNFDCCLGYTDRILHPKFIVGFTRQLANEGCDINAIIFHTKKKLSVCANPKQTWVKYIVRLLSKKVKN 69
                                    11        21        31        41        51        61        

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with CCL20_HUMAN | P78556 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:65
                                    40        50        60        70        80        90     
           CCL20_HUMAN   31 DCCLGYTDRILHPKFIVGFTRQLANEGCDINAIIFHTKKKLSVCANPKQTWVKYIVRLLSKKVKN 95
               SCOP domains d2hcib1 B:5-65 Macrophage inflammatory protein, MIP          ---- SCOP domains
               CATH domains 2hciB00 B:5-69  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeee.........eeeeee....eeee.................... Sec.struct. author
                 SAPs(SNPs) ----------------M------------------------------------------------ SAPs(SNPs)
                    PROSITE -SMALL_CYTOKINES_CC  PDB: B:6-49             -------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:5-38            -------------------------1.4b   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: B:38-64     ----- Transcript 1 (2)
                  2hci B  5 DCCLGYTDRILHPKFIVGFTRQLANEGCDINAIIFHTKKKLSVCANPKQTWVKYIVRLLSKKVKN 69
                                    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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HCI)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CCL20_HUMAN | P78556)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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: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:0071223    cellular response to lipoteichoic acid    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 lipoteichoic acid stimulus; lipoteichoic acid is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
    GO:0071310    cellular response to organic substance    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 organic substance 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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0050726    positive regulation of interleukin-1 alpha biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-1 alpha.
    GO:0051770    positive regulation of nitric-oxide synthase biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
    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.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        CCL20_HUMAN | P785561m8a 2jyo

(-) Related Entries Specified in the PDB File

1m8a THE SAME PROTEIN CRYSTAL STRUCTURE SOLVED IN P61 SPACE GROUP