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

(-) Description

Title :  STRUCTURE OF KLF4 ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH METHYLATED DNA
 
Authors :  Y. Liu, Y. O. Olanrewaju, R. M. Blumenthal, X. Zhang, X. Cheng
Date :  14 Aug 13  (Deposition) - 12 Feb 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Methylation, Transcription Factor, Cellular Reprogramming, C2H2 Zinc Finger, Dna Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, Y. O. Olanrewaju, Y. Zheng, H. Hashimoto, R. M. Blumenthal, X. Zhang, X. Cheng
Structural Basis For Klf4 Recognition Of Methylated Dna.
Nucleic Acids Res. V. 42 4859 2014
PubMed-ID: 24520114  |  Reference-DOI: 10.1093/NAR/GKU134

(-) Compounds

Molecule 1 - KRUEPPEL-LIKE FACTOR 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1248
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 396-483
    Gene: KLF4, EZF, GKLF, ZIE
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: EPITHELIAL ZINC FINGER PROTEIN EZF, GUT-ENRICHED KRUEPPEL- LIKE FACTOR
 
Molecule 2 - DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3')
    Chains: B
    Engineered: YES
    Other Details: DNA SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: DNA SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ACT1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:448 , ARG A:452 , THR A:455 , HIS A:457 , HOH A:665 , HOH A:668BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREARG A:452 , HOH A:603 , HOH A:652 , DA C:4BINDING SITE FOR RESIDUE ACT A 502
3AC3SOFTWARECYS A:462 , CYS A:465 , HIS A:478 , HIS A:482BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWARECYS A:432 , CYS A:437 , HIS A:450 , HIS A:454BINDING SITE FOR RESIDUE ZN A 504
5AC5SOFTWARECYS A:402 , CYS A:407 , HIS A:420 , HIS A:424BINDING SITE FOR RESIDUE ZN A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M9E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M9E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M9E)

(-) Exons   (0, 0)

(no "Exon" information available for 4M9E)

(-) 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:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4m9e A 399 THTCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF 483
                                   408       418       428       438       448       458       468       478     


Chain B from PDB  Type:DNA  Length:10
                                          
                 4m9e B   1 GAGGcGTGGC  10
                                |   10
                                5-5CM 


Chain C from PDB  Type:DNA  Length:10
                                          
                 4m9e C   1 GCCAcGCCTC  10
                                |   10
                                5-5CM
   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 4M9E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M9E)

(-) Gene Ontology  (81, 81)

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
    5CM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4m9e)
 

(-) 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
  4m9e
    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
  KLF4_MOUSE | Q60793
    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
  KLF4_MOUSE | Q60793
    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
        KLF4_MOUSE | Q60793: 2wbs 2wbu 5ke6 5ke7 5ke8 5ke9 5kea 5keb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4M9E)