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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RNGFI-B LIGAND-BINDING DOMAIN
 
Authors :  R. Flaig, H. Greschik, C. Peluso-Iltis, D. Moras, Structural Proteomics In Europe (Spine)
Date :  14 Jan 05  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Ngfi-B, Nur77, Nuclear Receptor, Ligand-Binding Domain, Novel Coregulator Interface, Cell-Specific, Structural Proteomics In Europe, Spine, Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Flaig, H. Greschik, C. Peluso-Iltis, D. Moras
Structural Basis For The Cell-Specific Activities Of The Ngfi-B And The Nurr1 Ligand-Binding Domain.
J. Biol. Chem. V. 280 19250 2005
PubMed-ID: 15716272  |  Reference-DOI: 10.1074/JBC.M413175200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORPHAN NUCLEAR RECEPTOR NR4A1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET-15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentLIGAND-BINDING DOMAIN
    GeneNR4A1, HMR, NGFIB
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymORPHAN NUCLEAR RECEPTOR HMR, NERVE GROWTH FACTOR INDUCED PROTEIN I-B, NGFI-B, NUR77, RNGFI-B

 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 1YJE)

(-) Sites  (0, 0)

(no "Site" information available for 1YJE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000101711ENSRNOE00000070711chr7:140012807-140012914108NR4A1_RAT-00--
1.2ENSRNOT000000101712ENSRNOE00000070817chr7:140015853-140016727875NR4A1_RAT1-2912910--
1.3ENSRNOT000000101713ENSRNOE00000071068chr7:140017539-140017668130NR4A1_RAT292-335440--
1.4ENSRNOT000000101714ENSRNOE00000071313chr7:140017970-140018121152NR4A1_RAT335-385511A:362-38524
1.5ENSRNOT000000101715ENSRNOE00000071534chr7:140018491-140018693203NR4A1_RAT386-453681A:386-45368
1.6ENSRNOT000000101716ENSRNOE00000071749chr7:140018783-140018961179NR4A1_RAT453-513611A:453-51361
1.7ENSRNOT000000101717ENSRNOE00000071997chr7:140019754-140020587834NR4A1_RAT513-597851A:513-594 (gaps)82

(-) 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:226
 aligned with NR4A1_RAT | P22829 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:233
                                   371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   
            NR4A1_RAT   362 NLLTSLIRAHLDSGPNTAKLDYSKFQELVLPRFGKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFGDWIDNILAFSRSLHSLGVDVPAFACLSALVLITDRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSRLLGKLPELRTLCTQGLQRIFCLKLEDLVPPPPIVDKIFMDT 594
               SCOP domains d1yjea_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains 1yjeA00 A:362-594 Retinoid X Receptor                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------Hormone_recep-1yjeA01 A:390-581                                                                                                                                                                 ------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:362-385Exon 1.5  PDB: A:386-453 UniProt: 386-453                           -----------------------------------------------------------Exon 1.7  PDB: A:513-594 (gaps) UniProt: 513-597 [INCOMPLETE]                      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------Exon 1.6  PDB: A:453-513 UniProt: 453-513                    --------------------------------------------------------------------------------- Transcript 1 (2)
                 1yje A 362 NLLTSLIRAHLDSGPNTAKLDYSKFQELVLPRFGKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCARGFGDWIDNILAFSRSLHSLGVDVPAFACLSALVLITDRHGLQDPRRVEELQNRIASCLKEHMAAV-------SCLSRLLGKLPELRTLCTQGLQRIFCLKLEDLVPPPPIVDKIFMDT 594
                                   371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   
                                                                                                                                                                                                             541     549                                             

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NR4A1_RAT | P22829)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0035259    glucocorticoid receptor binding    Interacting selectively and non-covalently with a glucocorticoid receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071376    cellular response to corticotropin-releasing hormone stimulus    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 corticotropin-releasing hormone stimulus. Corticotropin-releasing hormone is a peptide hormone involved in the stress response.
    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:0045444    fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0061469    regulation of type B pancreatic cell proliferation    Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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        NR4A1_RAT | P228291cit

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