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 1.5 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. 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 9330Homo sapiensMutation(s): 0 
Gene Names: CDK9CDC2L4TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens)
Explore P50750 
Go to UniProtKB:  P50750
GTEx:  ENSG00000136807 
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UniProt GroupP50750
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-T1264Homo sapiensMutation(s): 0 
Gene Names: CCNT1
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Find proteins for O60563 (Homo sapiens)
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Go to UniProtKB:  O60563
GTEx:  ENSG00000129315 
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UniProt GroupO60563
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AF4/FMR2 family member 436Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHB7 (Homo sapiens)
Explore Q9UHB7 
Go to UniProtKB:  Q9UHB7
PHAROS:  Q9UHB7
GTEx:  ENSG00000072364 
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UniProt GroupQ9UHB7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Tat58Human 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))
Explore P69697 
Go to UniProtKB:  P69697
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D 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

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
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description