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

(-) Description

Title :  CRYSTAL STRUCTURE OF NTRC4 DNA-BINDING DOMAIN BOUND TO DOUBLE-STRANDED DNA
 
Authors :  N. K. Vidangos, J. Heideker, A. Y. Lyubimov, M. Lamers, Y. Huo, J. G. Pelt J. D. Gralla, J. Kuriyan, J. M. Berger, D. E. Wemmer
Date :  27 Jun 12  (Deposition) - 29 Aug 12  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sigma-54, Transcriptional Activator, Dna-Binding Domain, Ntrc, Fis, Helix-Turn-Helix, Dna-Binding, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Vidangos, J. Heideker, A. Lyubimov, M. Lamers, Y. Huo, J. G. Pelton, J. Ton, J. Gralla, J. Berger, D. E. Wemmer
Dna Recognition By A Sigma (54) Transcriptional Activator From Aquifex Aeolicus.
J. Mol. Biol. V. 426 3553 2014
PubMed-ID: 25158097  |  Reference-DOI: 10.1016/J.JMB.2014.08.009

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: ROSETTA.PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 374-442)
    Gene: AQ_164, NTRC4
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
 
Molecule 2 - 5'-D(*AP*CP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP *GP*CP*AP*T)-3'
    Chains: C
    Engineered: YES
    Other Details: LPXC UPSTREAM DNA-BINDING SITE, FORWARD STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(P*GP*AP*TP*GP*CP*AP*TP*TP*TP*GP*CP*AP*AP*AP*TP*TP*TP*G P*CP*AP*A)-3'
    Chains: D
    Engineered: YES
    Other Details: LPXC UPSTREAM DNA-BINDING SITE, REVERSE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4FTH)

(-) Sites  (0, 0)

(no "Site" information available for 4FTH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FTH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FTH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FTH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FTH)

(-) Exons   (0, 0)

(no "Exon" information available for 4FTH)

(-) 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:68
                                                                                                   
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  4fth A 11 LKEKSWRDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVKS 78
                                    20        30        40        50        60        70        


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  4fth B 17 RDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVK 77
                                    26        36        46        56        66        76 


Chain C from PDB  Type:DNA  Length:21
                                                    
                  4fth C  1 CTTGCAAATTTGCAAATGCAT 21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                    
                  4fth D  1 GATGCATTTGCAAATTTGCAA 21
                                    10        20
   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  (0, 0)

(no "SCOP Domain" information available for 4FTH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FTH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FTH)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 4fth)
 
  Sites
(no "Sites" information available for 4fth)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fth)
 

(-) 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 ](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
  4fth
    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 2jrl 3dzd 3e7l

(-) Related Entries Specified in the PDB File

3e7l CRYSTAL STRUCTURE OF SIGMA-54 ACTIVATOR NTRC4'S DNA BINDING DOMAIN