4PMI

Crystal structure of Rev and Rev-response-element RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex.

Jayaraman, B.Crosby, D.C.Homer, C.Ribeiro, I.Mavor, D.Frankel, A.D.

(2014) Elife 4: e04120-e04120

  • DOI: 10.7554/eLife.04120
  • Primary Citation of Related Structures:  
    4PMI

  • PubMed Abstract: 
  • The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RN ...

    The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export-competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein-protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein RevBC72Human immunodeficiency virus type 1 (HXB3 ISOLATE)Mutation(s): 3 
Gene Names: rev
Find proteins for P69718 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB3))
Explore P69718 
Go to UniProtKB:  P69718
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Rev-Response-Element RNAA40Human immunodeficiency virus 1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.3α = 90
b = 165.3β = 90
c = 165.3γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building
SHELXDphasing

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 StatesP50GM082250

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2019-02-13
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence