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(-) Description

Title :  THE CRYSTAL STRUCTURE AND BIOLOGICAL FUNCTION OF LEUKEMIA INHIBITORY FACTOR: IMPLICATIONS FOR RECEPTOR BINDING
 
Authors :  R. C. Robinson, L. M. Grey, D. Staunton, D. I. Stuart, J. K. Heath, E. Y. Jones
Date :  12 Dec 94  (Deposition) - 31 Mar 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytokine, Four Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Robinson, L. M. Grey, D. Staunton, H. Vankelecom, A. B. Vernallis, J. F. Moreau, D. I. Stuart, J. K. Heath, E. Y. Jones
The Crystal Structure And Biological Function Of Leukemia Inhibitory Factor: Implications For Receptor Binding.
Cell(Cambridge, Mass. ) V. 77 1101 1994
PubMed-ID: 8020098  |  Reference-DOI: 10.1016/0092-8674(94)90449-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUKEMIA INHIBITORY FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PGEX-2T
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LKI)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:134
2A:18 -A:131
3A:60 -A:163

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:16 -Pro A:17
2Glu A:50 -Pro A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIF_OSMPS00590 LIF / OSM family signature.LIF_MOUSE174-193  1A:151-170

(-) Exons   (0, 0)

(no "Exon" information available for 1LKI)

(-) 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:172
 aligned with LIF_MOUSE | P09056 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:172
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  
            LIF_MOUSE    32 NATCAIRHPCHGNLMNQIKNQLAQLNGSANALFISYYTAQGEPFPNNVEKLCAPNMTDFPSFHGNGTEKTKLVELYRMVAYLSASLTNITRDQKVLNPTAVSLQVKLNATIDVMRGLLSNVLCRLCNKYRVGHVDVPPVPDHSDKEAFQRKKLGCQLLGTYKQVISVVVQAF 203
               SCOP domains d1lkia_ A: Leukemia inhibitory factor (LIF)                                                                                                                                  SCOP domains
               CATH domains 1lkiA00 A:9-180  [code=1.20.1250.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ------------LIF_OSM-1lkiA01 A:21-180                                                                                                                                         Pfam domains
         Sec.struct. author .eehhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee............hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------LIF_OSM             ---------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lki A   9 NATCAIRHPCHGNLMNQIKNQLAQLNGSANALFISYYTAQGEPFPNNVEKLCAPNMTDFPSFHGNGTEKTKLVELYRMVAYLSASLTNITRDQKVLNPTAVSLQVKLNATIDVMRGLLSNVLCRLCNKYRVGHVDVPPVPDHSDKEAFQRKKLGCQLLGTYKQVISVVVQAF 180
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: 4H_Cytokine (48)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIF_MOUSE | P09056)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0005146    leukemia inhibitory factor receptor binding    Interacting selectively and non-covalently with the leukemia inhibitory factor receptor.
    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.
    GO:0001135    transcription factor activity, RNA polymerase II transcription factor recruiting    The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
biological process
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0048708    astrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an astrocyte. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
    GO:0001974    blood vessel remodeling    The reorganization or renovation of existing blood vessels.
    GO:0046697    decidualization    The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta.
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    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:0048861    leukemia inhibitory factor signaling pathway    Any series of molecular signals initiated by the binding of leukemia inhibitory factor to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048286    lung alveolus development    The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0060463    lung lobe morphogenesis    The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung.
    GO:0060426    lung vasculature development    The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0048644    muscle organ morphogenesis    The process in which the anatomical structures of muscle are generated and organized.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0046888    negative regulation of hormone secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell.
    GO:0045835    negative regulation of meiotic nuclear division    Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0048711    positive regulation of astrocyte differentiation    Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051461    positive regulation of corticotropin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1901676    positive regulation of histone H3-K27 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K27 acetylation.
    GO:0045651    positive regulation of macrophage differentiation    Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
    GO:0072108    positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis    Any process that increases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0033141    positive regulation of peptidyl-serine phosphorylation of STAT protein    Any process that activates or increases the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:1900182    positive regulation of protein localization to nucleus    Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1903025    regulation of RNA polymerase II regulatory region sequence-specific DNA binding    Any process that modulates the frequency, rate or extent of RNA polymerase II regulatory region sequence-specific DNA binding.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0072307    regulation of metanephric nephron tubule epithelial cell differentiation    Any process that modulates the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0060708    spongiotrophoblast differentiation    The process in which a relatively unspecialized cell of the ectoplacental cone acquires specialized features of a spongiotrophoblast of the placenta. A spongiotrophoblast cell is a basophilic cell.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0060290    transdifferentiation    The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate.
    GO:0060707    trophoblast giant cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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        LIF_MOUSE | P09056: 1a7m

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