4OR5

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4.

Gu, J.Babayeva, N.D.Suwa, Y.Baranovskiy, A.G.Price, D.H.Tahirov, T.H.

(2014) Cell Cycle 13: 1788-1797

  • DOI: 10.4161/cc.28756
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Developing anti-viral therapies targeting HIV-1 transcription has been hampered by the limited structural knowledge of the proteins involved. HIV-1 hijacks the cellular machinery that controls RNA polymerase II elongation through an interaction of HI ...

    Developing anti-viral therapies targeting HIV-1 transcription has been hampered by the limited structural knowledge of the proteins involved. HIV-1 hijacks the cellular machinery that controls RNA polymerase II elongation through an interaction of HIV-1 Tat with the positive transcription elongation factor P-TEFb, which interacts with an AF4 family member (AFF1/2/3/4) in the super elongation complex (SEC). Because inclusion of Tat•P-TEFb into the SEC is critical for HIV transcription, we have determined the crystal structure of the Tat•AFF4•P-TEFb complex containing HIV-1 Tat (residues 1-48), human Cyclin T1 (1-266), human Cdk9 (7-332), and human AFF4 (27-69). Tat binding to AFF4•P-TEFb causes concerted structural changes in AFF4 via a shift of helix H5' of Cyclin T1 and the α-3 10 helix of AFF4. The interaction between Tat and AFF4 provides structural constraints that explain tolerated Tat mutations. Analysis of the Tat-binding surface of AFF4 coupled with modeling of all other AF4 family members suggests that AFF1 and AFF4 would be preferred over AFF2 or AFF3 for interaction with Tat•P-TEFb. The structure establishes that the Tat-TAR recognition motif (TRM) in Cyclin T1 interacts with both Tat and AFF4, leading to the exposure of arginine side chains for binding to TAR RNA. Furthermore, modeling of Tat Lys28 acetylation suggests that the acetyl group would be in a favorable position for H-bond formation with Asn257 of TRM, thereby stabilizing the TRM in Cyclin T1, and provides a structural basis for the modulation of TAR RNA binding by acetylation of Tat Lys28.


    Organizational Affiliation

    Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 9A, F326Homo sapiensMutation(s): 0 
Gene Names: CDK9CDC2L4TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for P50750 (Homo sapiens)
Explore P50750 
Go to UniProtKB:  P50750
NIH Common Fund Data Resources
PHAROS  P50750
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-T1B, G266Homo sapiensMutation(s): 0 
Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens)
Explore O60563 
Go to UniProtKB:  O60563
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PHAROS  O60563
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein TatC, H48HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: tat
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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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AF4/FMR2 family member 4E, J43Homo sapiensMutation(s): 0 
Gene Names: AFF4AF5Q31MCEFHSPC092
Find proteins for Q9UHB7 (Homo sapiens)
Explore Q9UHB7 
Go to UniProtKB:  Q9UHB7
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PHAROS  Q9UHB7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, F, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
YT3
Query on YT3

Download CCD File 
A, B, E, F, G, J
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
C, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A,FL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.862α = 90
b = 186.739β = 120.24
c = 108.661γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references