5L1Z

TAR complex with HIV-1 Tat-AFF4-P-TEFb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.

Schulze-Gahmen, U.Echeverria, I.Stjepanovic, G.Bai, Y.Lu, H.Schneidman-Duhovny, D.Doudna, J.A.Zhou, Q.Sali, A.Hurley, J.H.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.15910
  • Also Cited By: 6CYT

  • PubMed Abstract: 
  • HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR re ...

    HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn2+-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.


    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
330Homo 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
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
36Homo 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
58Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: tat
Find proteins for P69697 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P69697
Entity ID: 5
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')N23Human immunodeficiency virus 1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
ACE
Query on ACE
D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.870α = 90.00
b = 146.870β = 90.00
c = 103.750γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States--

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations