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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A TWO ZINC-FINGER PEPTIDE REVEALS AN EXTENSION TO THE RULES FOR ZINC-FINGER/DNA RECOGNITION
 
Authors :  L. Fairall, J. W. R. Schwabe, L. Chapman, J. T. Finch, D. Rhodes
Date :  06 Jun 94  (Deposition) - 31 Aug 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Protein-Dna Complex, Double Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Fairall, J. W. Schwabe, L. Chapman, J. T. Finch, D. Rhodes
The Crystal Structure Of A Two Zinc-Finger Peptide Reveals An Extension To The Rules For Zinc-Finger/Dna Recognition.
Nature V. 366 483 1993
PubMed-ID: 8247159  |  Reference-DOI: 10.1038/366483A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*TP*AP*AP*TP*AP*AP*GP*GP*AP*TP*AP*AP*CP*GP*TP*C P*CP*G)-3')
    Chains: B, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*CP*GP*GP*AP*CP*GP*TP*TP*AP*TP*CP*CP*TP*TP*AP*T P*TP*A)-3')
    Chains: C, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (TRAMTRACK DNA-BINDING DOMAIN)
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:113 , CYS A:116 , HIS A:129 , HIS A:134BINDING SITE FOR RESIDUE ZN A 171
2AC2SOFTWARECYS A:143 , CYS A:146 , HIS A:159 , HIS A:164BINDING SITE FOR RESIDUE ZN A 172
3AC3SOFTWARECYS D:113 , CYS D:116 , HIS D:129 , HIS D:134BINDING SITE FOR RESIDUE ZN D 173
4AC4SOFTWARECYS D:143 , CYS D:146 , HIS D:159 , HIS D:164BINDING SITE FOR RESIDUE ZN D 174

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TTKB_DROME510-531
 
540-561
 		  4A:113-134
D:113-134
A:143-164
D:143-164
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TTKB_DROME510-531
 
540-561
 		  2A:113-134
-
A:143-164
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TTKB_DROME510-531
 
540-561
 		  2-
D:113-134
-
D:143-164

(-) Exons   (0, 0)

(no "Exon" information available for 2DRP)

(-) 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:63
 aligned with TTKB_DROME | P17789 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:63
                                   509       519       529       539       549       559   
           TTKB_DROME   500 CTKEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIHK 562
               SCOP domains d2drpa1 A:103-139                    d2drpa2 A:140-165          SCOP domains
               CATH domains 2drpA01 A:103-136                 2drpA02 A:137-165             CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------ZINC_FINGER_C2H2_1    --------ZINC_FINGER_C2H2_1    - PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2drp A 103 FTKEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIHK 165
                                   112       122       132       142       152       162   


Chain B from PDB  Type:DNA  Length:19
                                                   
                 2drp B   1 CTAATAAGGATAACGTCCG  19
                                    10         


Chain C from PDB  Type:DNA  Length:19
                                                   
                 2drp C  21 TCGGACGTTATCCTTATTA  39
                                    30         


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with TTKB_DROME | P17789 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:65
                                   508       518       528       538       548       558     
           TTKB_DROME   499 YCTKEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIHKI 563
               SCOP domains d2drpd1 D:102-139                     d2drpd2 D:140-166           SCOP domains
               CATH domains -2drpD01 D:103-136                 2drpD02 D:137-165            - CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee.....ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------ZINC_FINGER_C2H2_1    --------ZINC_FINGER_C2H2_1    -- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2drp D 102 EFTKEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIHKI 166
                                   111       121       131       141       151       161     


Chain E from PDB  Type:DNA  Length:19
                                                   
                 2drp E   1 CTAATAAGGATAACGTCCG  19
                                    10         


Chain F from PDB  Type:DNA  Length:19
                                                   
                 2drp F  21 TCGGACGTTATCCTTATTA  39
                                    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  (1, 4)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (TTKB_DROME | P17789)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031208    POZ domain binding    Interacting selectively and non-covalently with a POZ (poxvirus and zinc finger) domain of a protein, a protein-protein interaction domain found in many transcription factors.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0048053    R1/R6 development    The process whose specific outcome is the progression of the R1 and R6 pair of photoreceptors in the eye over time, from their formation to the mature structures. R1 and R6 are paired photoreceptors that contribute to the outer rhabdomeres. An example of this process is found in Drosophila melanogaster.
    GO:0045467    R7 cell development    The process whose specific outcome is the progression of the R7 photoreceptor over time, from its formation to the mature structure. The R7 photoreceptor is the last photoreceptor to develop in the ommatidium.
    GO:0007298    border follicle cell migration    The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster.
    GO:0048854    brain morphogenesis    The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0035147    branch fusion, open tracheal system    Fusing of specific tracheal branches in an open tracheal system to branches from neighboring hemisegments to form a continuous tracheal network. Branch fusion is mediated by individual cells at the tip of each branch, which contact a similar cell and undergo a coordinated series of morphogenetic events that create a bicellular fusion joint.
    GO:0060446    branching involved in open tracheal system development    The process in which the anatomical structures of branches in the open tracheal system are generated and organized.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0040003    chitin-based cuticle development    Synthesis and deposition of a chitin-based noncellular, hardened, or membranous secretion from an epithelial sheet. An example of this process is found in Drosophila melanogaster.
    GO:0042675    compound eye cone cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a compound eye cone cell, a cone-shaped cell, that focuses light in a compound eye.
    GO:0048750    compound eye corneal lens morphogenesis    The process in which the anatomical structures of the compound eye corneal lens are generated and organized.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0046843    dorsal appendage formation    Establishment of the dorsal filaments, elaborate specializations of the chorion that protrude from the anterior end of the egg and facilitate embryonic respiration.
    GO:0035001    dorsal trunk growth, open tracheal system    Growth of epithelial tubes that originate from pits in an open tracheal system and grow towards each other to meet and form a continuous open tube called the dorsal trunk. The dorsal trunk extends from the anterior spiracle to the posterior spiracle of the larva and forms the main airway of the insect tracheal system.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0002121    inter-male aggressive behavior    Aggressive behavior based on competition between males of the same species over access to resources such as females, dominance, status, etc. and characterized by noise, threats, and is often less injurious.
    GO:0031987    locomotion involved in locomotory behavior    Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0030707    ovarian follicle cell development    The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster.
    GO:0007422    peripheral nervous system development    The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0042682    regulation of compound eye cone cell fate specification    Any process that mediates the specification of a cell into a compound eye cone cell.
    GO:0016476    regulation of embryonic cell shape    Any process that modulates the surface configuration of an embryonic cell.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035151    regulation of tube size, open tracheal system    Ensuring that an epithelial tube in an open tracheal system is of the correct length and diameter. Tracheal tubes undergo highly regulated tube-size increases during development, expanding up to 40 times their initial size by the end of larval life. Tube size appears to be controlled by regulation of apical membrane expansion and secretion, rather than by changes in cell number, size or shape.
    GO:0001964    startle response    An action or movement due to the application of a sudden unexpected stimulus.
    GO:0007426    tracheal outgrowth, open tracheal system    The projection of branches of an open tracheal system towards their target tissues. An example of this is found in Drosophila melanogaster.
    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.
    GO:0005700    polytene chromosome    A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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