4OGR

crystal structure of P-TEFb complex with AFF4 and Tat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter.

Schulze-Gahmen, U.Lu, H.Zhou, Q.Alber, T.

(2014) Elife 3: e02375-e02375

  • DOI: 10.7554/eLife.02375
  • Primary Citation of Related Structures:  
    4OGR

  • PubMed Abstract: 
  • Superelongation complexes (SECs) are essential for transcription elongation of many human genes, including the integrated HIV-1 genome. At the HIV-1 promoter, the viral Tat protein binds simultaneously to the nascent TAR RNA and the CycT1 subunit of the P-TEFb kinase in a SEC ...

    Superelongation complexes (SECs) are essential for transcription elongation of many human genes, including the integrated HIV-1 genome. At the HIV-1 promoter, the viral Tat protein binds simultaneously to the nascent TAR RNA and the CycT1 subunit of the P-TEFb kinase in a SEC. To understand the preferential recruitment of SECs by Tat and TAR, we determined the crystal structure of a quaternary complex containing Tat, P-TEFb, and the SEC scaffold, AFF4. Tat and AFF4 fold on the surface of CycT1 and interact directly. Interface mutations in the AFF4 homolog AFF1 reduced Tat-AFF1 affinity in vivo and Tat-dependent transcription from the HIV promoter. AFF4 binding in the presence of Tat partially orders the CycT1 Tat-TAR recognition motif and increases the affinity of Tat-P-TEFb for TAR 30-fold. These studies indicate that AFF4 acts as a two-step filter to increase the selectivity of Tat and TAR for SECs over P-TEFb alone.DOI: http://dx.doi.org/10.7554/eLife.02375.001.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 9A, D [auth E], G [auth I]332Homo sapiensMutation(s): 0 
Gene Names: CDK9CDC2L4TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens)
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PHAROS:  P50750
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-T1B, E [auth F], H [auth K]264Homo sapiensMutation(s): 0 
Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens)
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PHAROS:  O60563
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AF4/FMR2 family member 4C, F [auth G], I [auth L]75Homo sapiensMutation(s): 0 
Gene Names: AFF4AF5Q31MCEFHSPC092
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PHAROS:  Q9UHB7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein TatJ [auth D], K [auth H], L [auth M]58Human immunodeficiency virus type 1 (HXB3 ISOLATE)Mutation(s): 0 
Gene Names: tat
UniProt
Find proteins for P69698 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB3))
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Go to UniProtKB:  P69698
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.908α = 90
b = 184.908β = 90
c = 360.399γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description