5L1Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.90 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    5L1Z

  • 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 recognition motif (TRM) and the second Tat Zn 2+ -binding loop ...

    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 Zn 2+ -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

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 9A330Homo sapiensMutation(s): 0 
Gene Names: CDK9CDC2L4TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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Find proteins for P50750 (Homo sapiens)
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PHAROS:  P50750
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-T1B264Homo sapiensMutation(s): 0 
Gene Names: CCNT1
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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 4C36Homo sapiensMutation(s): 0 
Gene Names: AFF4AF5Q31MCEFHSPC092
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Find proteins for Q9UHB7 (Homo sapiens)
Explore Q9UHB7 
Go to UniProtKB:  Q9UHB7
PHAROS:  Q9UHB7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein TatD58Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: tat
UniProt
Find proteins for P69697 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
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Go to UniProtKB:  P69697
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
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')E [auth N]23Human immunodeficiency virus 1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth D], G [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.90 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.87α = 90
b = 146.87β = 90
c = 103.75γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2020-10-21
    Changes: Data collection, Derived calculations