3NTE | pdb_00003nte

Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding.

Du, S.Betts, L.Yang, R.Shi, H.Concel, J.Ahn, J.Aiken, C.Zhang, P.Yeh, J.I.

(2011) J Mol Biology 406: 371-386

  • DOI: https://doi.org/10.1016/j.jmb.2010.11.027
  • Primary Citation of Related Structures:  
    3NTE

  • PubMed Abstract: 

    The capsid (CA) protein plays crucial roles in HIV infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable, functional substrate-binding sites, the CA does not have a known site that affects catalytic or other innate activity, which can be more readily targeted in drug development efforts. We report the crystal structure of the HIV-1 CA, revealing the domain organization in the context of the wild-type full-length (FL) unassembled CA. The FL CA adopts an antiparallel dimer configuration, exhibiting a domain organization sterically incompatible with capsid assembly. A small compound, generated in situ during crystallization, is bound tightly at a hinge site ("H site"), indicating that binding at this interdomain region stabilizes the ADP conformation. Electron microscopy studies on nascent crystals reveal both dimeric and hexameric lattices coexisting within a single condition, in agreement with the interconvertibility of oligomeric forms and supporting the feasibility of promoting assembly-incompetent dimeric states. Solution characterization in the presence of the H-site ligand shows predominantly unassembled dimeric CA, even under conditions that promote assembly. Our structure elucidation of the HIV-1 FL CA and characterization of a potential allosteric binding site provides three-dimensional views of an assembly-defective conformation, a state targeted in, and thus directly relevant to, inhibitor development. Based on our findings, we propose an unprecedented means of preventing CA assembly, by "conformationally trapping" CA in assembly-incompetent conformational states induced by H-site binding.


  • Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh Medical School, Pittsburgh, PA 15260, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 capsid protein
A, B
221Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: CAgag
UniProt
Find proteins for Q77YG1 (Human immunodeficiency virus type 1)
Explore Q77YG1 
Go to UniProtKB:  Q77YG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ77YG1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3M
Query on I3M

Download Ideal Coordinates CCD File 
HA [auth B],
O [auth A]
Tri-iodode Anion
I3
WRTMQOHKMFDUKX-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]
CA [auth B]
D [auth A]
DA [auth B]
E [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
FE
Query on FE

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
IA [auth B]
JA [auth B]
KA [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
SA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.91α = 90
b = 86.532β = 99.73
c = 55.589γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted I3MClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-07-02
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary