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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TAL EFFECTOR DHAX3 BOUND TO DSDNA CONTAINING REPETITIVE METHYL-CPG
 
Authors :  N. Yan, D. Deng, C. Y. Yan, P. Yin, X. J. Pan, Y. G. Shi
Date :  10 Aug 12  (Deposition) - 03 Oct 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,G,H,I,J
Keywords :  Transcription Activition, Nucleus, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Yan, D. Deng, C. Y. Yan, P. Yin, X. J. Pan, Y. G. Shi
Crystal Structure Of A Protein Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HAX3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TAL EFFECTOR, UNP RESIDUES 231-720
    Gene: HAX3
    Mutation: YES
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. ARMORACIAE
    Organism Taxid: 329463
 
Molecule 2 - DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*CP*T)-3')
    Chains: I, G
    Engineered: YES
    Other Details: SENSE DNA
    Other Details - Source: SYNTHETIC DNA OLIGOS
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
    Chains: J, H
    Engineered: YES
    Other Details: ANTISENSE DNA
    Other Details - Source: SYNTHETIC DNA OLIGOS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
15CM4Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:832 , HOH A:1076 , HOH I:142 , HOH I:155 , HOH J:238 , HOH J:239BINDING SITE FOR RESIDUE MG J 101
2AC2SOFTWAREASP B:641 , HOH B:1041 , HOH B:1091 , HOH B:1109 , HOH H:108BINDING SITE FOR RESIDUE MG B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:251 -Pro A:252
2Pro B:251 -Pro B:252
3Ala B:285 -Pro B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GJP)

(-) 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:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjp A 230 MQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQALLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGRPALESIVAQLSRPDPALAALTNDHLVALACLGGRPALDAVKKLEHHHH 726
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       


Chain B from PDB  Type:PROTEIN  Length:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gjp B 231 QWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQALLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPQQVVAIASNGGGRPALESIVAQLSRPDALTNDHLVALACLGGRPALDAVKKLEH 723
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690 ||    704       714         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       692|                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        697                          


Chain G from PDB  Type:DNA  Length:15
                                               
                 4gjp G  -2 TGTCCCTTcGcGTCT  12
                                    |7|    
                                    6-5CM  
                                      8-5CM


Chain H from PDB  Type:DNA  Length:16
                                                
                 4gjp H -13 GAGACGCGAAGGGACA   2
                                    -4      


Chain I from PDB  Type:DNA  Length:17
                                                 
                 4gjp I  -2 TGTCCCTTcGcGTCTCT  14
                                    |7|      
                                    6-5CM    
                                      8-5CM  


Chain J from PDB  Type:DNA  Length:17
                                                 
                 4gjp J -14 AGAGACGCGAAGGGACA   2
                                    -5
   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 4GJP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4GJP)

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  Cis Peptide Bonds
    Ala B:285 - Pro B:286   [ RasMol ]  
    Pro A:251 - Pro A:252   [ RasMol ]  
    Pro B:251 - Pro B:252   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q3ZD72_XANCA | Q3ZD72: 4gg4 4gjr 4osh 4osi 4osj 4osk 4osl 4osm 4osq 4osr 4oss 4ost 4osv 4osw 4osz 4ot0 4ot3 4oto

(-) Related Entries Specified in the PDB File

4gg4 4gjr