Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE BERYLLOFLUORIDE-ACTIVATED NTRC4 RECEIVER DOMAIN DIMER
 
Authors :  C. Lee, E. Hong, M. Doucleff, J. G. Pelton, D. E. Wemmer, Berkeley Struc Genomics Center (Bsgc)
Date :  27 Jun 07  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Ntrc, Ntrc4, Receiver Domain, Transcription Regulator, Dimer, Structural Genomics, Berkeley Structural Genomics Center, Bsgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lee, M. Doucleff, E. Hong, J. Pelton, D. Wemmer
Solution Structure Of The Beryllofluoride-Activated Ntrc4 Receiver Domain Dimer.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: NTRC4, AQ_164
    Organism Scientific: AQUIFEX AEOLICUS
    Strain: VF5

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JRL)

(-) Sites  (0, 0)

(no "Site" information available for 2JRL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JRL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JRL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JRL)

(-) Exons   (0, 0)

(no "Exon" information available for 2JRL)

(-) Sequences/Alignments

NMR Structure
   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:121
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
         O66551_AQUAE     1 MKRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYS 121
               SCOP domains d2jrla_ A: automated matches                                                                                              SCOP domains
               CATH domains 2jrlA00 A:1-121  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.....eeeee..........hhhhhhhhh...eeeeee...hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jrl A   1 MKRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
         O66551_AQUAE     1 MKRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYS 121
               SCOP domains d2jrlb_ B: automated matches                                                                                              SCOP domains
               CATH domains 2jrlB00 B:1-121  [code=3.40.50.2300, no name defined]                                                                     CATH domains
           Pfam domains (1) ---Response_reg-2jrlB01 B:4-114                                                                                   ------- Pfam domains (1)
           Pfam domains (2) ---Response_reg-2jrlB02 B:4-114                                                                                   ------- Pfam domains (2)
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.....eeeee.........hhhhhhhhhh...eeeeee...hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jrl B   1 MKRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 2)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: CheY (97)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A,B   (O66551_AQUAE | O66551)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2jrl)
 
  Sites
(no "Sites" information available for 2jrl)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jrl)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2jrl
    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
  O66551_AQUAE | O66551
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  O66551_AQUAE | O66551
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O66551_AQUAE | O66551: 1zit 3dzd 3e7l 4fth

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JRL)