Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B
 
Authors :  G. Meinke, P. B. Sigler
Date :  05 Apr 99  (Deposition) - 03 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Orphan Nuclear Receptor, Early Immediate Response Gene Product, Transcription Factor, Monomeric Protein-Dna Complex, Minor Groove Interactions, Protein/Dna, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Meinke, P. B. Sigler
Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B.
Nat. Struct. Biol. V. 6 471 1999
PubMed-ID: 10331876  |  Reference-DOI: 10.1038/8276
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (ORPHAN NUCLEAR RECEPTOR NGFI-B)
    Cellular Location: NUCLEUS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: DNA-BINDING DOMAIN AND C-TERMINAL EXTENSION
    Organ: BRAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NGFI-B

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:232 , CYS A:235 , CYS A:249 , CYS A:252BINDING SITE FOR RESIDUE ZN A 398
2AC2SOFTWARECYS A:268 , CYS A:274 , CYS A:284 , CYS A:287BINDING SITE FOR RESIDUE ZN A 399
3ZNAAUTHORZN A:398 , CYS A:232 , CYS A:235 , CYS A:249 , CYS A:252ZINC COORDINATED BY 4 CYSTEINES
4ZNBAUTHORZN A:399 , CYS A:268 , CYS A:274 , CYS A:284 , CYS A:287ZINC COORDINATED BY 4 CYSTEINES

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEAR_REC_DBD_1PS00031 Nuclear hormones receptors DNA-binding region signature.NR4A1_RAT266-292  1A:232-258

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000101711ENSRNOE00000070711chr7:140012807-140012914108NR4A1_RAT-00--
1.2ENSRNOT000000101712ENSRNOE00000070817chr7:140015853-140016727875NR4A1_RAT1-2912911A:230-25728
1.3ENSRNOT000000101713ENSRNOE00000071068chr7:140017539-140017668130NR4A1_RAT292-335441A:258-30144
1.4ENSRNOT000000101714ENSRNOE00000071313chr7:140017970-140018121152NR4A1_RAT335-385511A:301-31818
1.5ENSRNOT000000101715ENSRNOE00000071534chr7:140018491-140018693203NR4A1_RAT386-453680--
1.6ENSRNOT000000101716ENSRNOE00000071749chr7:140018783-140018961179NR4A1_RAT453-513610--
1.7ENSRNOT000000101717ENSRNOE00000071997chr7:140019754-140020587834NR4A1_RAT513-597850--

(-) 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:89
 aligned with NR4A1_RAT | P22829 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:89
                                   273       283       293       303       313       323       333       343         
            NR4A1_RAT   264 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 352
               SCOP domains d1cita_ A: Orphan nuclear receptor NGFI-B DNA-binding domain                              SCOP domains
               CATH domains 1citA00 A:230-318 Erythroid Transcription Factor GATA-1, subunit A                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eee.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --NUCLEAR_REC_DBD_1          ------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:230-257    Exon 1.3  PDB: A:258-301 UniProt: 292-335   ----------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.4           Transcript 1 (2)
                 1cit A 230 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKP 318
                                   239       249       259       269       279       289       299       309         


Chain B from PDB  Type:DNA  Length:16
                                                
                 1cit B 402 CCGAAAAGGTCATGCG 417
                                   411      


Chain C from PDB  Type:DNA  Length:16
                                                
                 1cit C 419 CGCATGACCTTTTCGG 434
                                   428
   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: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) 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:0003700    DNA-binding transcription factor activity    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
    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:0004879    nuclear receptor activity    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: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:0001077    proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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 by RNA polymerase II    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 by RNA polymerase II    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    ZNA  [ RasMol ]  +environment [ RasMol ]
    ZNB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cit)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cit
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NR4A1_RAT | P22829
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NR4A1_RAT | P22829
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NR4A1_RAT | P22829: 1yje

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CIT)