1TF6

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.308 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.

Nolte, R.T.Conlin, R.M.Harrison, S.C.Brown, R.S.

(1998) Proc Natl Acad Sci U S A 95: 2938-2943

  • DOI: https://doi.org/10.1073/pnas.95.6.2938
  • Primary Citation of Related Structures:  
    1TF6

  • PubMed Abstract: 

    The crystal structure of the six NH2-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound with 31 bp of the 5S rRNA gene promoter has been determined at 3.1 A resolution. Individual zinc fingers are positioned differently in the major groove and across the minor groove of DNA to span the entire length of the duplex. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove.


  • Organizational Affiliation

    Harvard Medical School, Boston, MA 02115, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (TRANSCRIPTION FACTOR IIIA)E [auth A],
F [auth D]
190Xenopus laevisMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')A [auth B],
C [auth E]
31N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')B [auth C],
D [auth F]
31N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.308 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.18α = 90.07
b = 64.712β = 92.98
c = 78.035γ = 102.95
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RAVEphasing
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-10
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations