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(-) Description

Title :  AART, A SIX FINGER ZINC FINGER DESIGNED TO RECOGNIZE ANN TRIPLETS
 
Authors :  N. C. Horton, D. J. Segal, M. Bhakta, J. W. Crotty, C. F. Barbas Iii
Date :  12 Aug 06  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Dna Binding, Zinc Finger, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Segal, J. W. Crotty, M. S. Bhakta, C. F. Barbas, N. C. Horton
Structure Of Aart, A Designed Six-Finger Zinc Finger Peptide, Bound To Dna.
J. Mol. Biol. V. 363 405 2006
PubMed-ID: 16963084  |  Reference-DOI: 10.1016/J.JMB.2006.08.016

(-) Compounds

Molecule 1 - 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP *CP*GP*GP*G)-3'
    ChainsC, E
    EngineeredYES
    Other DetailsSOLID PHASE SYNTHESIS BY PHOSPHORAMIDITE CHEMISTRY
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP *AP*TP*CP*T)-3'
    ChainsD, F
    EngineeredYES
    Other DetailsSOLID PHASE SYNTHESIS BY PHOSPHORAMIDITE CHEMISTRY
    SyntheticYES
 
Molecule 3 - AART
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL FUSION
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A CD  
Biological Unit 2 (1x) B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN11Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:40 , HIS A:44BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWARECYS A:80 , CYS A:83 , HIS A:96 , HIS A:100BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWARECYS A:108 , CYS A:111 , HIS A:124 , HIS A:128BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWARECYS A:136 , CYS A:139 , HIS A:152 , HIS A:156BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWARECYS A:164 , CYS A:167 , HIS A:180 , HIS A:184BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWARECYS A:52 , CYS A:55 , HIS A:68 , HIS A:72BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWARECYS B:24 , CYS B:27 , HIS B:40 , HIS B:44BINDING SITE FOR RESIDUE ZN B 507
08AC8SOFTWARECYS B:80 , CYS B:83 , HIS B:96 , HIS B:100BINDING SITE FOR RESIDUE ZN B 508
09AC9SOFTWARECYS B:108 , CYS B:111 , HIS B:124 , HIS B:128BINDING SITE FOR RESIDUE ZN B 509
10BC1SOFTWARECYS B:136 , CYS B:139 , HIS B:152 , HIS B:156BINDING SITE FOR RESIDUE ZN B 510
11BC2SOFTWARECYS B:52 , CYS B:55 , HIS B:68 , HIS B:72BINDING SITE FOR RESIDUE ZN B 512
12BC3SOFTWAREASN A:92 , HOH A:572 , DA C:12 , DA C:13 , DA C:14 , DT D:10BINDING SITE FOR RESIDUE GOL C 601
13BC4SOFTWAREHIS A:120 , ARG A:145 , DG C:10 , DG C:11 , HOH C:635 , HOH C:643 , DC D:13 , HOH D:71BINDING SITE FOR RESIDUE GOL C 602
14BC5SOFTWAREASN B:92 , HOH B:602 , DA E:12 , DA E:13 , DA E:14 , DT F:10 , HOH F:31BINDING SITE FOR RESIDUE GOL E 603
15BC6SOFTWAREHIS B:120 , DG E:10 , DG E:11 , DC F:13BINDING SITE FOR RESIDUE GOL E 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I13)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I13)

(-) PROSITE Motifs  (1, 14)

Asymmetric Unit (1, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZSCA2_MOUSE224-244
252-272
 
280-300
 
308-328
 
336-356
 
364-384
392-412
420-440
 
448-468
476-496
504-524
532-552
560-580
588-608
  14B:24-44
A:52-72
B:52-72
A:80-100
B:80-100
A:108-128
B:108-128
A:136-143
B:136-153
-
B:154-156
A:144-152
B:173-174
-
A:153-156
A:164-184
-
-
-
Biological Unit 1 (1, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZSCA2_MOUSE224-244
252-272
 
280-300
 
308-328
 
336-356
 
364-384
392-412
420-440
 
448-468
476-496
504-524
532-552
560-580
588-608
  7-
A:52-72
-
A:80-100
-
A:108-128
-
A:136-143
-
-
-
A:144-152
-
-
A:153-156
A:164-184
-
-
-
Biological Unit 2 (1, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZSCA2_MOUSE224-244
252-272
 
280-300
 
308-328
 
336-356
 
364-384
392-412
420-440
 
448-468
476-496
504-524
532-552
560-580
588-608
  7B:24-44
-
B:52-72
-
B:80-100
-
B:108-128
-
B:136-153
-
B:154-156
-
B:173-174
-
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2I13)

(-) Sequences/Alignments

Asymmetric 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:151
 aligned with ZSCA2_MOUSE | Q07230 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:294
                                   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    
          ZSCA2_MOUSE   231 FSRKSHLITHERTHTGEKYYKCDECGKSFSDGSNFSRHQTTHTGEKPYKCRDCGKSFSRSANLITHQRIHTGEKPFQCAECGKSFSRSPNLIAHQRTHTGEKPYSCPECGKSFGNRSSLNTHQGIHTGEKPYACKECGESFSYNSNLIRHQRIHTGEKPYKCTECGQKFSQSSALITHRRTHTGEKPYQCGECGKNFSRSSNLATHRRTHLVEKPYKCGLCGKSFSQSSSLIAHQGTHTGEKPYECLTCGESFSWSSNLIKHQRTHTGEKPYRCGDCGKGFSQRSQLVVHQRTH 524
               SCOP domains d2i13a1 A:31-1   84 AART, designed six-finger protein                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.---..ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee------------------------------------------------------------------------------------.hhhhhhhh--------------------------------------------------------hhhhhh...ee......ee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ZINC_FINGER_C2-------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i13 A  31 FSRSDHLAEHQRTH---KPYKCPECGKSFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEKPYKCPECGKSF------------------------------------------------------------------------------------SREDNLHTH--------------------------------------------------------QRTHTGEKPYKCPECGKSFSRRDALNVHQRTH 184
                                    40   |   |50        60        70        80        90       100       110       120       130       140  |      -         -         -         -         -         -         -         -       146     |   -         -         -         -         -         -  |    160       170       180    
                                        44  48                                                                                            143                                                                                  144     152                                                      153                               

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with ZSCA2_MOUSE | Q07230 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:223
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439   
          ZSCA2_MOUSE   220 KPYECPQCGKTFSRKSHLITHERTHTGEKYYKCDECGKSFSDGSNFSRHQTTHTGEKPYKCRDCGKSFSRSANLITHQRIHTGEKPFQCAECGKSFSRSPNLIAHQRTHTGEKPYSCPECGKSFGNRSSLNTHQGIHTGEKPYACKECGESFSYNSNLIRHQRIHTGEKPYKCTECGQKFSQSSALITHRRTHTGEKPYQCGECGKNFSRSSNLATHRRTHLV 442
               SCOP domains -----------d2i13b1 B:31-178 AART, designed six-finger protein                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhh--------------------------------------------------------h...-----------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i13 B  20 KPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQ--------------------------------------------------------RTHT-----------------------RRDALN 178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149   |     -         -         -         -         -         -|  |     -         -       175   
                                                                                                                                                               153                                                      154  |                     173     
                                                                                                                                                                                                                           157                             

Chain C from PDB  Type:DNA  Length:22
                                                      
                 2i13 C   1 CAGATGTAGGGAAAAGCCCGGG  22
                                    10        20  

Chain D from PDB  Type:DNA  Length:22
                                                      
                 2i13 D   1 GCCCGGGCTTTTCCCTACATCT  22
                                    10        20  

Chain E from PDB  Type:DNA  Length:22
                                                      
                 2i13 E   1 CAGATGTAGGGAAAAGCCCGGG  22
                                    10        20  

Chain F from PDB  Type:DNA  Length:22
                                                      
                 2i13 F   1 GCCCGGGCTTTTCCCTACATCT  22
                                    10        20  

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I13)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ZSCA2_MOUSE | Q07230)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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