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 

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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: https://doi.org/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: CDK9, CDC2L4, TAK
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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UniProt GroupP50750
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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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AF4/FMR2 family member 4C36Homo sapiensMutation(s): 0 
Gene Names: AFF4, AF5Q31, MCEF, HSPC092
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PHAROS:  Q9UHB7
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UniProt GroupQ9UHB7
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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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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
Protein Feature View
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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		A L-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

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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