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(-) Description

Title :  MOUSE KLF4 E446P ZNF1-3 AND MPG/MPG SEQUENCE DNA COMPLEX STRUCTURE
 
Authors :  H. Hashimoto, X. Cheng
Date :  09 Jun 16  (Deposition) - 14 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Klf4, Zinc Finger, Kruppel-Like Factors, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, D. Wang, A. N. Steves, P. Jin, R. M. Blumenthal, X. Zhang, X. Cheng
Distinctive Klf4 Mutants Determine Preference For Dna Methylation Status.
Nucleic Acids Res. V. 44 10177 2016
PubMed-ID: 27596594  |  Reference-DOI: 10.1093/NAR/GKW774

(-) Compounds

Molecule 1 - KRUEPPEL-LIKE FACTOR 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-6P-1
    Fragment: UNP RESIDUES 396-483
    Gene: KLF4, EZF, GKLF, ZIE
    Mutation: YES
    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
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:462 , CYS A:465 , HIS A:478 , HIS A:482binding site for residue ZN A 501
2AC2SOFTWARECYS A:432 , CYS A:437 , HIS A:450 , HIS A:454binding site for residue ZN A 502
3AC3SOFTWARECYS A:402 , CYS A:407 , HIS A:420 , HIS A:424binding site for residue ZN A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KE8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KE8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KE8)

(-) Exons   (0, 0)

(no "Exon" information available for 5KE8)

(-) 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    
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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.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5ke8 A 399 THTCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDPLTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF 483
                                   408       418       428       438       448       458       468       478     


Chain B from PDB  Type:DNA  Length:10
                                          
                 5ke8 B   1 GAGGxGTGGC  10
                                |   10
                                5-5CM 


Chain C from PDB  Type:DNA  Length:10
                                          
                 5ke8 C   1 GCCAxGCCTC  10
                                |   10
                                5-5CM
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  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 5KE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KE8)

(-) Gene Ontology  (81, 81)

Asymmetric/Biological Unit(hide GO term definitions)

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  KLF4_MOUSE | Q60793
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 Related Entries

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

UniProtKB/Swiss-Prot
        KLF4_MOUSE | Q60793: 2wbs 2wbu 4m9e 5ke6 5ke7 5ke9 5kea 5keb

(-) Related Entries Specified in the PDB File

5k5h 5k5i 5k5j 5k5l 5ke9 5kea 5keb