6CYT

HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex.

Schulze-Gahmen, U.Hurley, J.H.

(2018) Proc Natl Acad Sci U S A 115: 12973-12978

  • DOI: 10.1073/pnas.1806438115
  • Primary Citation of Related Structures:  
    6CYT

  • PubMed Abstract: 
  • Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II ...

    Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II. Structural studies of TAR interactions have been largely focused on interactions between the TAR bulge and the arginine-rich motif (ARM) of Tat. Here, the crystal structure of the TAR loop in complex with Tat and the SEC core was determined at a 3.5-Å resolution. The bound TAR loop is stabilized by cross-loop hydrogen bonds. It makes structure-specific contacts with the side chains of the Cyclin T1 Tat-TAR recognition motif (TRM) and the zinc-coordinating loop of Tat. The TAR loop phosphate backbone forms electrostatic and VDW interactions with positively charged side chains of the CycT1 TRM. Mutational analysis showed that these interactions contribute importantly to binding affinity. The Tat ARM was present in the crystallized construct; however, it was not visualized in the electron density, and the TAR bulge was not formed in the RNA construct used in crystallization. Binding assays showed that TAR bulge-Tat ARM interactions contribute less to TAR binding affinity than TAR loop interactions with the CycT1 TRM and Tat core. Thus, the TAR loop evolved to make high-affinity interactions with the TRM while Tat has three roles: scaffolding and stabilizing the TRM, making specific interactions through its zinc-coordinating loop, and making electrostatic interactions through its ARM.


    Related Citations: 
    • 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: --

    Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 9A332Homo 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
PHAROS:  P50750
GTEx:  ENSG00000136807 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50750
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-T1B264Homo sapiensMutation(s): 0 
Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens)
Explore O60563 
Go to UniProtKB:  O60563
PHAROS:  O60563
GTEx:  ENSG00000129315 
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UniProt GroupO60563
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AF4/FMR2 family member 4C36Homo sapiensMutation(s): 0 
Gene Names: AFF4AF5Q31MCEFHSPC092
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
MoleculeChainsSequence LengthOrganismDetailsImage
Protein TatD58Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: tat
UniProt
Find proteins for P04608 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04608 
Go to UniProtKB:  P04608
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UniProt GroupP04608
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3')E [auth N]20Human 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
A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.58α = 90
b = 148.58β = 90
c = 104.63γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

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 StatesP50GM0882250

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence