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 :  HOXB13-MEIS1 HETERODIMER BOUND TO DNA
 
Authors :  E. Morgunova, Y. Yin, A. Jolma, A. Popov, J. Taipale
Date :  26 Oct 15  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Transcription Factor, Heterodimer, Complex, Bound To Dna, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Morgunova, Y. Yin, A. Jolma, A. Popov, J. Taipale
Molecular Basis Of Recognition Of Two Distinct Dna Sequence By A Single Transcription Factor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN MEIS2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETG20A
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 284-338
    Gene: MEIS2, MRG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MEIS1-RELATED PROTEIN 1
 
Molecule 2 - DNA (5'- D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - HOMEOBOX PROTEIN HOX-B13
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETG20A
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 217-277
    Gene: HOXB13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5EG0)

(-) Sites  (0, 0)

(no "Site" information available for 5EG0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EG0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:279 -Pro A:280
2Ala B:276 -Lys B:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EG0)

(-) Exons   (0, 0)

(no "Exon" information available for 5EG0)

(-) 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:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 5eg0 A 279 APKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM 334
                                   288       298       308       318       328      


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.hhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5eg0 B 217 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKVLAK 277
                                   226       236       246       256       266       276 


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5eg0 D  20 GTTGACAGTTTTACGAGG  37
                                    29        


Chain E from PDB  Type:DNA  Length:18
                                                  
                 5eg0 E   1 CCTCGTAAAACTGTCAAC  18
                                    10
   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 5EG0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EG0)

(-) Gene Ontology  (34, 40)

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 5eg0)
 
  Sites
(no "Sites" information available for 5eg0)
 
  Cis Peptide Bonds
    Ala A:279 - Pro A:280   [ RasMol ]  
    Ala B:276 - Lys B:277   [ RasMol ]  
 

(-) 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
  5eg0
    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
  HXB13_HUMAN | Q92826
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MEIS2_HUMAN | O14770
    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
  HXB13_HUMAN | Q92826
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MEIS2_HUMAN | O14770
    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
        HXB13_HUMAN | Q92826: 2cra 5edn 5eea 5ef6 5ego
        MEIS2_HUMAN | O14770: 3k2a 4xrm 5bng

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5EG0)