6BHR | pdb_00006bhr

HIV-1 immature CTD-SP1 hexamer in complex with IP6

• PDB DOI: https://doi.org/10.2210/pdb6BHR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-31 Released: 2018-08-08 
• Deposition Author(s): Zadrozny, K., Wagner, J.M., Ganser-Pornillos, B.K., Pornillos, O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Inositol phosphates are assembly co-factors for HIV-1.

Dick, R.A., Zadrozny, K.K., Xu, C., Schur, F.K.M., Lyddon, T.D., Ricana, C.L., Wagner, J.M., Perilla, J.R., Ganser-Pornillos, B.K., Johnson, M.C., Pornillos, O., Vogt, V.M.

(2018) Nature 560: 509-512

• PubMed: 30069050 
• DOI: https://doi.org/10.1038/s41586-018-0396-4
• Primary Citation Related Structures: 
  6BHR, 6BHS, 6BHT


• PubMed Abstract: 
  

  A short, 14-amino-acid segment called SP1, located in the Gag structural protein ¹ , has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane ^2,3 . Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors ^4,5 . Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP ₆ ) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP ₆ makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP ₆ interaction promotes the assembly of the mature capsid lattice. These studies identify IP ₆ as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. [e-mail].
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Department of Chemistry and Biochemistry, University of Delaware, Newport, DE, USA.
Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
Institute of Science and Technology Austria, Klosterneuburg, Austria.
Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. [e-mail].
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

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: 11.14 kDa 
• Atom Count: 705 
• Modeled Residue Count: 91 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24,Spacer peptide 1	A [auth G]	95	Human immunodeficiency virus type 1 BH10	Mutation(s): 0
UniProt
Find proteins for P03347 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03347  Go to UniProtKB:  P03347

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	B [auth G]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.939	α = 90
b = 70.939	β = 90
c = 42.041	γ = 120

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: 2018-08-08 
Deposition Author(s): Zadrozny, K., Wagner, J.M., Ganser-Pornillos, B.K., Pornillos, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI129678
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM103297

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2018-09-05
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2020-10-14
  Changes: Structure summary
• Version 1.6: 2023-10-04
  Changes: Data collection, Database references, Refinement description