1NH2 | pdb_00001nh2

Crystal structure of a yeast TFIIA/TBP/DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1NH2

This is version 1.4 of the entry. See complete history. 

Literature

Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes.

Bleichenbacher, M., Tan, S., Richmond, T.J.

(2003) J Mol Biology 332: 783-793

  • DOI: https://doi.org/10.1016/s0022-2836(03)00887-8
  • Primary Citation Related Structures: 
    1NH2, 1NVP

  • PubMed Abstract: 

    RNA polymerase II-dependent transcription requires the assembly of a multi-protein, preinitiation complex on core promoter elements. Transcription factor IID (TFIID) comprising the TATA box-binding protein (TBP) and TBP-associated factors (TAFs) is responsible for promoter recognition in this complex. Subsequent association of TFIIA and TFIIB provides enhanced complex stability. TFIIA is required for transcriptional stimulation by certain viral and cellular activators, and favors formation of the preinitiation complex in the presence of repressor NC2. The X-ray structures of human and yeast TBP/TFIIA/DNA complexes at 2.1A and 1.9A resolution, respectively, are presented here and seen to resemble each other closely. The interactions made by human TFIIA with TBP and DNA within and upstream of the TATA box, including those involving water molecules, are described and compared to the yeast structure. Of particular interest is a previously unobserved region of TFIIA that extends the binding interface with TBP in the yeast, but not in the human complex, and that further elucidates biochemical and genetic results.

    • Organizational Affiliation: 
    • ETH Zürich, Institute for Molecular Biology and Biophysics, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 58.53 kDa 
  • Atom Count: 4,204 
  • Modeled Residue Count: 412 
  • Deposited Residue Count: 465 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIIDC [auth A]180Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15 OR BTF1 OR YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P13393
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UniProt GroupP13393
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large chainD [auth B]53Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA1 OR YOR194C
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32773 
Go to UniProtKB:  P32773
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UniProt GroupP32773
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large chainE [auth C]79Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA1 OR YOR194C
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32773 
Go to UniProtKB:  P32773
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UniProt GroupP32773
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA small chainF [auth D]121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA2 OR YKL058W
UniProt
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32774 
Go to UniProtKB:  P32774
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UniProt GroupP32774
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)P*AP*AP*AP*AP*C)-3'A [auth E]16N/A
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3'B [auth F]16N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.01α = 90
b = 92.02β = 90
c = 117.017γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection