4IMY

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.

Schulze-Gahmen, U., Upton, H., Birnberg, A., Bao, K., Chou, S., Krogan, N.J., Zhou, Q., Alber, T.

(2013) Elife 2: e00327-e00327

  • DOI: 10.7554/eLife.00327

  • PubMed Abstract: 

    • Human positive transcription elongation factor b (P-TEFb) phosphorylates RNA polymerase II and regulatory proteins to trigger elongation of many gene transcripts. The HIV-1 Tat protein selectively recruits P-TEFb as part of a super elongation complex ...

    Human positive transcription elongation factor b (P-TEFb) phosphorylates RNA polymerase II and regulatory proteins to trigger elongation of many gene transcripts. The HIV-1 Tat protein selectively recruits P-TEFb as part of a super elongation complex (SEC) organized on a flexible AFF1 or AFF4 scaffold. To understand this specificity and determine if scaffold binding alters P-TEFb conformation, we determined the structure of a tripartite complex containing the recognition regions of P-TEFb and AFF4. AFF4 meanders over the surface of the P-TEFb cyclin T1 (CycT1) subunit but makes no stable contacts with the CDK9 kinase subunit. Interface mutations reduced CycT1 binding and AFF4-dependent transcription. AFF4 is positioned to make unexpected direct contacts with HIV Tat, and Tat enhances P-TEFb affinity for AFF4. These studies define the mechanism of scaffold recognition by P-TEFb and reveal an unanticipated intersubunit pocket on the AFF4 SEC that potentially represents a target for therapeutic intervention against HIV/AIDS. DOI:http://dx.doi.org/10.7554/eLife.00327.001.

    Organizational Affiliation: 

    Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 9
A, C, E
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, D, F
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
G, H, I
75Homo sapiensMutation(s): 0 
Gene Names: AFF4 (AF5Q31, MCEF)
Find proteins for Q9UHB7 (Homo sapiens)
Go to Gene View: AFF4
Go to UniProtKB:  Q9UHB7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download SDF File 
Download CCD File 
A, C, E
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C, E
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.691α = 90.00
b = 126.298β = 90.00
c = 195.626γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references