5I2D

Crystal structure of T. thermophilus TTHB099 class II transcription activation complex: TAP-RPo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription activation.

Feng, Y.Zhang, Y.Ebright, R.H.

(2016) Science 352: 1330-1333

  • DOI: 10.1126/science.aaf4417
  • Primary Citation of Related Structures:  
    5I2D

  • PubMed Abstract: 
  • Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, ...

    Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σ(A) holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B, L, M315Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoATTHA1664
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHR6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC, N1119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D, O1524Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE, P99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF, Q443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: sigATTHA0532
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator, Crp familyG, H, R, S215Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHB099
Find proteins for Q53W63 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q53W63
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (72-MER)J, U72Thermus thermophilus
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 9
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*CP*GP*A)-3')K, V4Thermus thermophilus
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    Entity ID: 7
    MoleculeChainsLengthOrganismImage
    DNA (72-MER)I, T72Thermus thermophilus
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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    D, O
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    D, O
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 4.41 Å
    • R-Value Free: 0.284 
    • R-Value Work: 0.241 
    • R-Value Observed: 0.242 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 171.487α = 90
    b = 105.446β = 102.39
    c = 374.585γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    MOLREPphasing

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM041376

    Revision History 

    • Version 1.0: 2016-06-22
      Type: Initial release
    • Version 1.1: 2017-09-13
      Changes: Author supporting evidence, Derived calculations
    • Version 1.2: 2019-12-25
      Changes: Author supporting evidence