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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF TAL EFFECTOR PTHXO1 BOUND TO ITS DNA TARGET
 
Authors :  A. N. S. Mak, P. Bradley, R. A. Cernadas, A. J. Bogdanove, B. L. Stoddard
Date :  02 Nov 11  (Deposition) - 04 Jan 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Tal Effector, Transcription-Dna Complex, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Mak, P. Bradley, R. A. Cernadas, A. J. Bogdanove, B. L. Stoddard
The Crystal Structure Of Tal Effector Pthxo1 Bound To Its Dna Target.
Science V. 335 716 2012
PubMed-ID: 22223736  |  Reference-DOI: 10.1126/SCIENCE.1216211

(-) Compounds

Molecule 1 - TAL EFFECTOR AVRBS3/PTHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 21-1043
    GenePTHXO1, PXO_00227
    Organism ScientificXANTHOMONAS ORYZAE
    Organism Taxid360094
    StrainPXO99A
 
Molecule 2 - DNA-1
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES
 
Molecule 3 - DNA-2
    ChainsC
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3UGM)

(-) Sites  (0, 0)

(no "Site" information available for 3UGM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UGM)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu A:203 -Gly A:204
2Gly A:204 -Thr A:205
3His A:212 -Ile A:213
4Val A:1041 -Ala A:1042
5Asn A:1046 -Ser A:1047

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UGM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UGM)

(-) Exons   (0, 0)

(no "Exon" information available for 3UGM)

(-) 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:854
 aligned with PTHX1_XANOP | B2SU53 from UniProtKB/Swiss-Prot  Length:1373

    Alignment length:880
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048
         PTHX1_XANOP    169 KPKVGSTVAQHHEALVGHGFTHAHIVALSRHPAALGTVAVKYQDMIAALPEATHEDIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLVKIAKRGGVTAVEAVHASRNALTGAPLNLTPAQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETMQRLLPVLCQAHGLPPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQTHGLTPAQVVAIASHDGGKQALETVQQLLPVLCQAHGLTPDQVVAIASNIGGKQALATVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTQVQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTQEQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNIGGKQALETVQRLLPVLCQDHGLTLAQVVAIASNIGGKQALETVQRLLPVLCQAHGLTQDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTLDQVVAIASNGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNSG 1048
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------.-..------...........................--.hhhhhhhhh...hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh--....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhh.------..hhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhh...........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhh--..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ugm A  169 KPKVR-------E-LV------AHIVALSQHPAALGTVAVTYQHIITAL--ATHEDIVGVGKQWSGARALEALLTDAGELRGPPLQLDTGQLVKIAKRGGVTAMEAVHASRNALT--PLNLTPAQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETMQRLLPVLCQAHGLPPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQTHGLTPAQVVAIASHDGGKQALETVQQLLPVLCQAHGLTPDQVVAIASNIGGKQALATVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTQVQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLP------GLTQEQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNIGGKQALETVQRLLPVLCQDHGLTLAQVVAIASNIGGKQALETVQRLLPVLCQ--GLTQDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTLDQVVAIASNGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNSG 1048
                                |    -  | ||   -  |    198       208        |- |     228       238       248       258       268       278    |  288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788 |     798       808       818       828       838       848       858       868       878       888       898       908       918       928 |  |  938       948       958       968       978       988       998      1008      1018      1028      1038      1048
                              173     181 ||    191                       217  |                                                            283  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     790    797                                                                                                                                  930  |                                                                                                                   
                                        183|                                 220                                                               286                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    933                                                                                                                   
                                         184                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                

Chain B from PDB  Type:DNA  Length:38
                                                                       
                3ugm B   -6 TAGATATGCATCTCCCCCTACTGTACACCACCAAAAGT   31
                                     3        13        23        

Chain C from PDB  Type:DNA  Length:38
                                                                       
                3ugm C    1 TTTTGGTGGTGTACAGTAGGGGGAGATGCATATCTAAC   38
                                    10        20        30        

   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 3UGM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UGM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UGM)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTHX1_XANOP | B2SU53)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0034053    modulation by symbiont of host defense-related programmed cell death    Any process in which an organism modulates the frequency, rate or extent of defense-related programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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  Cis Peptide Bonds
    Asn A:1046 - Ser A:1047   [ RasMol ]  
    Gly A:204 - Thr A:205   [ RasMol ]  
    His A:212 - Ile A:213   [ RasMol ]  
    Leu A:203 - Gly A:204   [ RasMol ]  
    Val A:1041 - Ala A:1042   [ RasMol ]  
 

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