2HGH

Transcription Factor IIIA zinc fingers 4-6 bound to 5S rRNA 55mer (NMR structure)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Induced Fit and 'Lock and Key' Recognition of 5 S RNA by Zinc Fingers of Transcription Factor IIIA

Lee, B.M., Xu, J., Clarkson, B.K., Martinez-Yamout, M.A., Dyson, J.H., Case, D.A., Gottesfeld, J.M., Wright, P.E.

(2006) J Mol Biol 357: 275-291

  • DOI: 10.1016/j.jmb.2005.12.010
  • Primary Citation of Related Structures:  
    2HGH

  • PubMed Abstract: 

    • Transcription factor IIIA (TFIIIA) is a Cys2His2 zinc finger protein that regulates expression of the 5 S ribosomal RNA gene by binding specifically to the internal control element. TFIIIA also functions in transport and storage of 5 S RNA by binding directly to the RNA transcript ...

    Transcription factor IIIA (TFIIIA) is a Cys2His2 zinc finger protein that regulates expression of the 5 S ribosomal RNA gene by binding specifically to the internal control element. TFIIIA also functions in transport and storage of 5 S RNA by binding directly to the RNA transcript. To obtain insights into the mechanism by which TFIIIA recognizes 5 S RNA, we determined the solution structure of the middle three zinc fingers bound to the central core of 5 S RNA. Finger 4 utilizes "lock and key" recognition to bind in the widened major groove of the pre-structured RNA loop E motif. This interaction is mediated by direct hydrogen bonding interactions with bases. In contrast, recognition of loop A, a flexible junction of three helices, occurs by an induced fit mechanism that involves reorganization of the conserved CAUA motif and structuring of the finger 5-finger 6 interface to form a complementary RNA binding surface.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor IIIAB [auth A]87Xenopus laevisMutation(s): 0 
Gene Names: gtf3a
UniProt
Find proteins for P03001 (Xenopus laevis)
Explore P03001 
Go to UniProtKB:  P03001
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03001
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
55-MERA [auth B]55N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2HGH Olderado

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-06-27 
  • Released Date: 2006-08-01 
    • Deposition Author(s): Lee, B.M.

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations