5I4T | pdb_00005i4t

Immature hexagonal lattice of HIV-1 Gag

• PDB DOI: https://doi.org/10.2210/pdb5I4T/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-12 Released: 2016-07-27 
• Deposition Author(s): Pornillos, O., Wagner, J.M., Zadrozny, K., Ganser-Pornillos, B.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 
  0.278 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an HIV assembly and maturation switch.

Wagner, J.M., Zadrozny, K.K., Chrustowicz, J., Purdy, M.D., Yeager, M., Ganser-Pornillos, B.K., Pornillos, O.

(2016) Elife 5

• PubMed: 27416583 
• DOI: https://doi.org/10.7554/eLife.17063
• Primary Citation Related Structures: 
  5I4T


• PubMed Abstract: 
  

  Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate.

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Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States.
Department of Medicine, Division of Cardiovascular Medicine, University of Virginia Health System, Charlottesville, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.16 kDa 
• Atom Count: 3,865 
• Modeled Residue Count: 546 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTD-SP1 fragment of HIV-1 Gag	A [auth G], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L]	110	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for Q72497 (Human immunodeficiency virus type 1) Explore Q72497  Go to UniProtKB:  Q72497

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free:  0.278 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.959	α = 90
b = 122.733	β = 94.3
c = 85.414	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Pornillos, O., Wagner, J.M., Zadrozny, K., Ganser-Pornillos, B.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description