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(-) Description

Title :  CILIARY NEUROTROPHIC FACTOR
 
Authors :  N. Q. Mcdonald, N. Panayotatos, W. A. Hendrickson
Date :  06 Jun 96  (Deposition) - 26 Mar 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  1,2,3,4
Biol. Unit 1:  1,4  (1x)
Biol. Unit 2:  2,3  (1x)
Keywords :  Cytokine, Neurotrophic Factor, Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Q. Mcdonald, N. Panayotatos, W. A. Hendrickson
Crystal Structure Of Dimeric Human Ciliary Neurotrophic Factor Determined By Mad Phasing.
Embo J. V. 14 2689 1995
PubMed-ID: 7796798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CILIARY NEUROTROPHIC FACTOR
    Chains1, 2, 3, 4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneHUMAN CNTF
    Expression System PlasmidCLASSIFIED
    Expression System Taxid562
    GeneHUMAN CNTF
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCNTF

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit 1234
Biological Unit 1 (1x)1  4
Biological Unit 2 (1x) 23 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2YB1Ligand/IonYTTERBIUM (III) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2YB-1Ligand/IonYTTERBIUM (III) ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2YB-1Ligand/IonYTTERBIUM (III) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU 2:164 , GLN 2:167 , HOH 2:931 , SO4 3:189BINDING SITE FOR RESIDUE YB 3 188
2AC2SOFTWARELYS 2:160 , GLU 2:164 , ARG 3:25 , ILE 3:173 , ARG 3:177 , YB 3:188BINDING SITE FOR RESIDUE SO4 3 189
3AC3SOFTWAREHIS 1:12 , ARG 1:13 , ARG 1:14 , THR 1:184 , HOH 1:192 , HOH 1:194 , HOH 1:830BINDING SITE FOR RESIDUE SO4 1 190
4AC4SOFTWAREARG 1:25 , ARG 1:28 , ILE 1:173 , HOH 1:875BINDING SITE FOR RESIDUE SO4 1 191
5AC5SOFTWARETRP 2:168 , ARG 3:25 , ARG 3:177 , HOH 3:952BINDING SITE FOR RESIDUE SO4 3 192

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013924H182RCNTF_HUMANPolymorphism62661/2/3H182R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013924H182RCNTF_HUMANPolymorphism62661H182R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013924H182RCNTF_HUMANPolymorphism62662/3H182R

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CNT)

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003619871ENSE00002164401chr11:58390146-58390339194CNTF_HUMAN1-383841:11-38
2:12-38
3:11-38
4:12-38
28
27
28
27
1.2ENST000003619872ENSE00002185716chr11:58391507-583931981692CNTF_HUMAN39-20016241:39-187 (gaps)
2:39-187 (gaps)
3:39-182 (gaps)
4:39-180 (gaps)
149
149
144
142

(-) 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 1 from PDB  Type:PROTEIN  Length:150
 aligned with CNTF_HUMAN | P26441 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:177
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
           CNTF_HUMAN    11 PHRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVASTDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHDLRFISSHQTGIP 187
               SCOP domains d1cnt1_ 1: Ciliary neurotrophic fa                   ctor (CNTF)                                                                                                                  SCOP domains
               CATH domains 1cnt100 1:11-187  [code=1.20.1250.                   10, no name defined]                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.............--------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 1:11-38      Exon 1.2  PDB: 1:39-187 (gaps) UniProt: 39-200 [INCOMPLETE]                                                                                           Transcript 1
                 1cnt 1  11 PHRRDLCSRSIWLARKIRSDLTALTESYVKHQGL-------------------WSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADGM--------LFEKKLWGLKVLQELSQWTVRSIHDLRFISSHQTGIP 187
                                    20        30        40   |     -         -   |    70        80        90       100       110       120       130       140 |       -|      160       170       180       
                                                            44                  64                                                                           142      151                                    

Chain 2 from PDB  Type:PROTEIN  Length:130
 aligned with CNTF_HUMAN | P26441 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:176
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           CNTF_HUMAN    12 HRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVASTDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHDLRFISSHQTGIP 187
               SCOP domains d1cnt2_ 2: Ciliary neurotrophic f                      actor (CNTF)                                                                                                              SCOP domains
               CATH domains 1cnt200 2:12-187  [code=1.20.1250                      .10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------------------..hhhhhhhhhhhhhhhhhhhhhh.----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh........--------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 2:12-38     Exon 1.2  PDB: 2:39-187 (gaps) UniProt: 39-200 [INCOMPLETE]                                                                                           Transcript 1
                 1cnt 2  12 HRRDLCSRSIWLARKIRSDLTALTESYVKHQGL----------------------LTEAERLQENLQAYRTFHVLLARLL----------EGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRN--------------FEKKLWGLKVLQELSQWTVRSIHDLRFISSHQTGIP 187
                                    21        31        41  |      -         -     |  71        81        91         -|      111       121       131     |   -         -|      161       171       181      
                                                           44                     67                      91        102                                137            152                                   

Chain 3 from PDB  Type:PROTEIN  Length:146
 aligned with CNTF_HUMAN | P26441 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:172
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           CNTF_HUMAN    11 PHRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVASTDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHDLRFISSH 182
               SCOP domains d1cnt3_ 3: Ciliary neurotrophic fa                   ctor (CNTF)                                                                                                             SCOP domains
               CATH domains 1cnt300 3:11-182  [code=1.20.1250.                   10, no name defined]                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhh..-------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh............-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 3:11-38      Exon 1.2  PDB: 3:39-182 (gaps) UniProt: 39-200 [INCOMPLETE]                                                                                      Transcript 1
                 1cnt 3  11 PHRRDLCSRSIWLARKIRSDLTALTESYVKHQGL-------------------WSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADG-------GGLFEKKLWGLKVLQELSQWTVRSIHDLRFISSH 182
                                    20        30        40   |     -         -   |    70        80        90       100       110       120       130       140|      150       160       170       180  
                                                            44                  64                                                                          141     149                                 

Chain 4 from PDB  Type:PROTEIN  Length:126
 aligned with CNTF_HUMAN | P26441 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:169
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           CNTF_HUMAN    12 HRRDLCSRSIWLARKIRSDLTALTESYVKHQGLNKNINLDSADGMPVASTDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRNEADGMPINVGDGGLFEKKLWGLKVLQELSQWTVRSIHDLRFIS 180
               SCOP domains d1cnt4_ 4: Ciliary neurotrophic f                     actor (CNTF)                                                                                                        SCOP domains
               CATH domains 1cnt400 4:12-180  [code=1.20.1250                     .10, no name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------------...hhhhhhhhhhhhhhhhhhhhhhhhhh.------.hhhhhhhhhhhhhhhhhhhhhhhhhhh........----------------.hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 4:12-38     Exon 1.2  PDB: 4:39-180 (gaps) UniProt: 39-200 [INCOMPLETE]                                                                                    Transcript 1
                 1cnt 4  12 HRRDLCSRSIWLARKIRSDLTALTESYVKHQGL---------------------ELTEAERLQENLQAYRTFHVLLARLLEDQQ------EGDFHQAIHTLLLQVAAFAYQIEELMILLEYKIPRN----------------KKLWGLKVLQELSQWTVRSIHDLRFIS 180
                                    21        31        41  |      -         -    |   71        81        91   |     -|      111       121       131     |   -         -  |    161       171         
                                                           44                    66                           95    102                                137              154                          

   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 Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain 1,2,3,4   (CNTF_HUMAN | P26441)
molecular function
    GO:0005127    ciliary neurotrophic factor receptor binding    Interacting selectively and non-covalently with the ciliary neurotrophic factor receptor.
    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:0005138    interleukin-6 receptor binding    Interacting selectively and non-covalently with the interleukin-6 receptor.
    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:0048143    astrocyte activation    A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0070120    ciliary neurotrophic factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a ciliary neurotrophic factor (CNTF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0048644    muscle organ morphogenesis    The process in which the anatomical structures of muscle are generated and organized.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0046533    negative regulation of photoreceptor cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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:0048680    positive regulation of axon regeneration    Any process that activates, maintains or increases the rate of axon regeneration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0046668    regulation of retinal cell programmed cell death    Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina.
    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:0097058    CRLF-CLCF1 complex    A heterodimeric protein complex that is composed of cardiotrophin-like cytokine factor 1 (product of the CLCF1 gene) and cytokine receptor-like factor 1 (product of the CRLF gene) and is secreted into the extracellular space. The CRLF-CLCF1 complex is a ligand for the ciliary neurotrophic factor (CNTF) receptor complex.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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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