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(-) Description

Title :  MACROPHAGE MIGRATION INHIBITORY FACTOR
 
Authors :  M. Suzuki, H. Sugimoto, A. Nakagawa, I. Tanaka
Date :  31 Jan 96  (Deposition) - 11 Jul 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Macrophage, Inflammatory Response, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Suzuki, H. Sugimoto, A. Nakagawa, I. Tanaka, J. Nishihira, M. Sakai
Crystal Structure Of The Macrophage Migration Inhibitory Factor From Rat Liver.
Nat. Struct. Biol. V. 3 259 1996
PubMed-ID: 8605628  |  Reference-DOI: 10.1038/NSB0396-259
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3
    Expression System Taxid562
    MutationYES
    OrganLIVER
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsSELENOMETHIONYL PROTEIN (MET 47)
    Other Details - SourceMETHIONINE AUXOTROPIC ESCHERICHIA COLI STRAINS HARVESTED IN A MEDIUM CONTAINING SELENOMETHIONINE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1FIM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FIM)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.MIF_RAT55-69  1A:54-68
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.MIF_RAT55-69  3A:54-68

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000086081ENSRNOE00000267950chr20:13191986-13192177192MIF_RAT1-36361A:1-3535
1.2ENSRNOT000000086082ENSRNOE00000355764chr20:13192370-13192542173MIF_RAT37-94581A:36-9358
1.3ENSRNOT000000086083ENSRNOE00000060442chr20:13192665-13192851187MIF_RAT94-115221A:93-10311

(-) 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:103
 aligned with MIF_RAT | P30904 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
              MIF_RAT     2 PMFIVNTNVPRASVPEGFLSELTQQLAQATGKPAQYIAVHVVPDQLMTFSGTSDPCALCSLHSIGKIGGAQNRNYSKLLCGLLSDRLHISPDRVYINYYDMNA 104
               SCOP domains d1fima_ A: Microphage migration inhibition factor (MIF)                                                 SCOP domains
               CATH domains 1fimA00 A:1-103 Macrophage Migration Inhibitory Factor                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee.............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ----------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-35 UniProt: 1-36Exon 1.2  PDB: A:36-93 UniProt: 37-94                     ---------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.3    Transcript 1 (2)
                 1fim A   1 PAFIVNTNVPRASVPEGFLSELTQQLAQATGKPAQYIAVHVVPDQLmTFSGTSDPCALCSLHSIGKIGGAQNRNYSKLLCGLLSDRLHISPDRVYINYYDANA 103
                                    10        20        30        40      | 50        60        70        80        90       100   
                                                                         47-MSE                                                    

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FIM)

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain A   (MIF_RAT | P30904)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0004167    dopachrome isomerase activity    Catalysis of the reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0050178    phenylpyruvate tautomerase activity    Catalysis of the reaction: keto-phenylpyruvate = enol-phenylpyruvate.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0002035    brain renin-angiotensin system    The process in which an angiotensin-mediated signaling system present in the brain regulates the force with which blood passes through the circulatory system.
    GO:0070301    cellular response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0042756    drinking behavior    The specific behavior of an organism relating to the intake of liquids, especially water.
    GO:0001942    hair follicle development    The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002675    positive regulation of acute inflammatory response    Any process that activates or increases the frequency, rate, or extent of an acute inflammatory response.
    GO:0048680    positive regulation of axon regeneration    Any process that activates, maintains or increases the rate of axon regeneration.
    GO:0046326    positive regulation of glucose import    Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:0045821    positive regulation of glycolytic process    Any process that activates or increases the frequency, rate or extent of glycolysis.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0043268    positive regulation of potassium ion transport    Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0014911    positive regulation of smooth muscle cell migration    Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0009408    response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0010035    response to inorganic substance    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 inorganic substance stimulus.
    GO:0032868    response to insulin    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 insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    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:0009612    response to mechanical 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 a mechanical stimulus.
    GO:0032572    response to menaquinone    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 menaquinone (vitamin K2) stimulus.
    GO:0032570    response to progesterone    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 progesterone stimulus.
    GO:0033197    response to vitamin E    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 E stimulus.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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