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(-) Description

Title :  CRYSTAL STRUCTURE OF ZNF217 BOUND TO DNA
 
Authors :  M. S. Vandevenne, D. A. Jacques, J. M. Guss, J. P. Mackay
Date :  08 Nov 11  (Deposition) - 05 Dec 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Zinc Finger, Transcription Factor, Dna Binding, Dna-Metal Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Vandevenne, D. A. Jacques, J. M. Guss, J. P. Mackay
Rediscovering Dna Recognition By Classical Zinc Fingers.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP *CP*A)-3'
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*AP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP *CP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - ZINC FINGER PROTEIN 217
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGERS 6 AND 7 (UNP RESIDUES 469-523)
    Gene: ZNF217, ZABC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSCRIPTION FACTOR ZNF217

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2ZN8Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:501 , CYS C:504 , HIS C:517 , HIS C:522BINDING SITE FOR RESIDUE ZN C 967
2AC2SOFTWARECYS C:473 , CYS C:476 , HIS C:489 , HIS C:493BINDING SITE FOR RESIDUE ZN C 968
3AC3SOFTWARECYS D:501 , CYS D:504 , HIS D:517 , HIS D:522BINDING SITE FOR RESIDUE ZN D 967
4AC4SOFTWARECYS D:473 , CYS D:476 , HIS D:489 , HIS D:493BINDING SITE FOR RESIDUE ZN D 968
5AC5SOFTWAREDA A:13 , HIS C:521BINDING SITE FOR RESIDUE ZN C 1
6AC6SOFTWAREDG B:12 , HOH B:51BINDING SITE FOR RESIDUE ZN B 21
7AC7SOFTWAREGLU C:502 , GLU D:472 , GLY D:477 , HIS D:521BINDING SITE FOR RESIDUE ZN D 1
8AC8SOFTWAREDT B:17 , HOH B:53 , HOH D:50BINDING SITE FOR RESIDUE ZN B 22

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UK3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UK3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UK3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZN217_HUMAN67-88
130-150
158-178
218-238
377-397
473-493
 		  2-
-
-
-
-
C:473-493
D:473-493

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4ENST000003714714ENSE00001523402chr20:52210378-5221029584ZN217_HUMAN-00--
1.5bENST000003714715bENSE00002162750chr20:52199707-521980001708ZN217_HUMAN1-4564560--
1.6ENST000003714716ENSE00001722637chr20:52194989-52194873117ZN217_HUMAN456-495402C:471-495
D:470-495		25
26
1.7aENST000003714717aENSE00001742197chr20:52193819-521922661554ZN217_HUMAN495-10135192C:495-522
D:495-523		28
29
1.8ENST000003714718ENSE00001143007chr20:52188392-52188260133ZN217_HUMAN1013-1048360--
1.9dENST000003714719dENSE00001455296chr20:52185803-521836042200ZN217_HUMAN-00--

(-) 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:DNA  Length:20
                                                    
                 3uk3 A   1 TTTGCAGAATCGATTCTGCA  20
                                    10        20


Chain B from PDB  Type:DNA  Length:20
                                                    
                 3uk3 B   1 AATGCAGAATCGATTCTGCA  20
                                    10        20


Chain C from PDB  Type:PROTEIN  Length:52
 aligned with ZN217_HUMAN | O75362 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:52
                                   480       490       500       510       520  
          ZN217_HUMAN   471 RECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHH 522
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE --ZINC_FINGER_C2H2_1   ----------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: C:471-495 --------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.7a  PDB: C:495-522    Transcript 1 (2)
                 3uk3 C 471 RECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHH 522
                                   480       490       500       510       520  


Chain D from PDB  Type:PROTEIN  Length:54
 aligned with ZN217_HUMAN | O75362 from UniProtKB/Swiss-Prot  Length:1048

    Alignment length:54
                                   479       489       499       509       519    
          ZN217_HUMAN   470 SRECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHHK 523
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1   ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6  PDB: D:470-495  ---------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.7a  PDB: D:495-523     Transcript 1 (2)
                 3uk3 D 470 SRECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHHK 523
                                   479       489       499       509       519
   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 3UK3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UK3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UK3)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (ZN217_HUMAN | O75362)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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: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:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ZN217_HUMAN | O75362: 2hu2 4f2j 4is1

(-) Related Entries Specified in the PDB File

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