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(-) Description

Title :  TRANSCRIPTION FACTOR IIIA ZINC FINGERS 4-6 BOUND TO 5S RRNA 55MER (NMR STRUCTURE)
 
Authors :  B. M. Lee
Date :  27 Jun 06  (Deposition) - 01 Aug 06  (Release) - 14 Apr 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Zinc Finger, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Lee, J. Xu, B. K. Clarkson, M. A. Martinez-Yamout, J. H. Dyson, D. A. Case, J. M. Gottesfeld, P. E. Wright
Induced Fit And 'Lock And Key' Recognition Of 5 S Rna By Zinc Fingers Of Transcription Factor Iiia
J. Mol. Biol. V. 357 275 2006
PubMed-ID: 16405997  |  Reference-DOI: 10.1016/J.JMB.2005.12.010

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR IIIA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGERS 4-6 (RESIDUES 127-212)
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: FACTOR A, TFIIIA, S-TFIIIA/O-TFIIIA
 
Molecule 2 - 55-MER
    Chains: B
    Engineered: YES
    Other Details: RNA WAS SYNTHESIZED BY IN VITRO TRANSCRIPTION FROM LINEARIZED PUC18 PLASMID CONTAINING THE 55MER SEQUENCE AND THE PRIMER BINDING SITE FOR T7 RNA POLYMERASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:107 , CYS A:112 , HIS A:125 , HIS A:129BINDING SITE FOR RESIDUE ZN A 191
2AC2SOFTWARECYS A:137 , CYS A:142 , HIS A:155 , HIS A:159BINDING SITE FOR RESIDUE ZN A 192
3AC3SOFTWARECYS A:164 , CYS A:170 , HIS A:183 , HIS A:188BINDING SITE FOR RESIDUE ZN A 193

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TF3A_XENLA37-59
67-89
97-120
129-151
159-181
216-236
245-268
276-298		  2-
-
-
A:107-129
A:137-159
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2HGH)

(-) Sequences/Alignments

NMR Structure
   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:87
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:87
                                   135       145       155       165       175       185       195       205       
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d2hgha1 A:104-131           d2hgha2 A:132-160            d2hgha3 A:161-190              SCOP domains
               CATH domains 2hghA01 A:104-132            2hghA02 A:133-161            2hghA03 A:162-190             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhhhee.........ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2hgh A 104 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   113       123       133       143       153       163       173       183       


Chain B from PDB  Type:RNA  Length:55
                                                                                       
                 2hgh B   1 GGGCCAUACCUCUUGGGCCUGGUUAGUACCUCUUCGGUGGGAAUACCAGGUGCCC  55
                                    10        20        30        40        50
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 3)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (TF3A_XENLA | P03001)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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.
biological process
    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: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
        TF3A_XENLA | P03001: 1tf3 1tf6 1un6 2j7j

(-) Related Entries Specified in the PDB File

1tf3 1znf