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 :  WILMS TUMOR PROTEIN (WT1) ZINC FINGERS IN COMPLEX WITH HYDROXYMETHYLATED DNA
 
Authors :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Chen
Date :  12 Aug 14  (Deposition) - 08 Oct 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Zinc Finger, Transcription, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Cheng
Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence.
Genes Dev. V. 28 2304 2014
PubMed-ID: 25258363  |  Reference-DOI: 10.1101/GAD.250746.114

(-) Compounds

Molecule 1 - WILMS TUMOR PROTEIN, ISOFORM 4/CRA_A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1, PXC1295
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER 2-4
    Gene: WT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: WT33
 
Molecule 2 - DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2EDO2Ligand/Ion1,2-ETHANEDIOL
3ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:355 , CYS A:360 , HIS A:373 , HIS A:377BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:385 , CYS A:388 , HIS A:401 , HIS A:405BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARECYS A:413 , CYS A:418 , HIS A:431 , HIS A:435BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWARETYR A:353 , ARG A:366 , SER A:367 , HOH B:142 , DC C:61 , HOH C:216BINDING SITE FOR RESIDUE EDO A 504
5AC5SOFTWAREARG A:366 , ASP A:368 , ARG A:372 , 5HC B:9 , 5HC C:53 , DG C:54BINDING SITE FOR RESIDUE EDO C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R2P)

(-) Exons   (0, 0)

(no "Exon" information available for 4R2P)

(-) 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
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4r2p A 349 SEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR 437
                                   358       368       378       388       398       408       418       428         


Chain B from PDB  Type:DNA  Length:11
                                           
                 4r2p B   1 AGCGTGGGcGT  11
                                    10 
                                    9-5HC


Chain C from PDB  Type:DNA  Length:11
                                           
                 4r2p C  51 TAcGCCCACGC  61
                              |     60 
                              |        
                             53-5HC
   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 4R2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R2P)

(-) Gene Ontology  (65, 65)

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
    5HC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 4r2p)
 

(-) 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
  4r2p
    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
  WT1_HUMAN | P19544
    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
  WT1_HUMAN | P19544
    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
        WT1_HUMAN | P19544: 1lu6 1xf7 2g7t 2g7v 2g7w 2g7x 2jp9 2jpa 2prt 3hpj 3myj 4r2e 4r2q 4r2r 4r2s 4wuu 5kl2 5kl3 5kl4 5kl5 5kl6 5kl7

(-) Related Entries Specified in the PDB File

4r2a 4r2c 4r2d 4r2e 4r2q 4r2r 4r2s