4OGR

crystal structure of P-TEFb complex with AFF4 and Tat

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 

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


  • 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 ...

    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 uschulze-gahmen@berkeley.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 9
A, E, I
332Homo sapiensMutation(s): 0 
Gene Names: CDK9 (CDC2L4, TAK)
EC: 2.7.11.22, 2.7.11.23
Find proteins for P50750 (Homo sapiens)
Go to Gene View: CDK9
Go to UniProtKB:  P50750
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-T1
B, F, K
264Homo sapiensMutation(s): 0 
Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens)
Go to Gene View: CCNT1
Go to UniProtKB:  O60563
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AF4/FMR2 family member 4
C, G, L
75Homo sapiensMutation(s): 0 
Gene Names: AFF4 (AF5Q31, MCEF)
Find proteins for Q9UHB7 (Homo sapiens)
Go to Gene View: AFF4
Go to UniProtKB:  Q9UHB7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein Tat
D, H, M
58Human immunodeficiency virus type 1 group M subtype B (isolate HXB3)Mutation(s): 0 
Gene Names: tat
Find proteins for P69698 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB3))
Go to UniProtKB:  P69698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
D, H, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN
Download SDF File 
Download CCD File 
A, E, I
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, E, I
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
ACE
Query on ACE
D, H, M
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 184.908α = 90.00
b = 184.908β = 90.00
c = 360.399γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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