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
  • Primary Citation of Related Structures:  
    4OR5

  • 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 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) ...

    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 LengthOrganismDetailsImage
Cyclin-dependent kinase 9A, E [auth F]326Homo 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-T1B, F [auth G]266Homo 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
Protein TatC, G [auth H]48HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: tat
UniProt
Find proteins for P04608 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AF4/FMR2 family member 4D [auth E], H [auth J]43Homo sapiensMutation(s): 0 
Gene Names: AFF4AF5Q31MCEFHSPC092
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Find proteins for Q9UHB7 (Homo sapiens)
Explore 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 Ideal Coordinates CCD File 
CA [auth G], L [auth A], P [auth B], Y [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
YT3
Query on YT3

Download Ideal Coordinates CCD File 
AA [auth G] , BA [auth G] , FA [auth J] , I [auth A] , J [auth A] , K [auth A] , M [auth B] , N [auth B] , 
AA [auth G],  BA [auth G],  FA [auth J],  I [auth A],  J [auth A],  K [auth A],  M [auth B],  N [auth B],  O [auth B],  S [auth E],  T [auth E],  U [auth F],  V [auth F],  W [auth F],  X [auth F],  Z [auth G]
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth H], EA [auth H], Q [auth C], R [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, E [auth F]L-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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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