8GDV

Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6

• PDB DOI: https://doi.org/10.2210/pdb8GDV/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-03-06 Released: 2024-03-13 
• Deposition Author(s): Briganti, L., Schope, L., Kvaratskhelia, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.347 
• R-Value Work: 0.307 
• R-Value Observed: 0.309 

Literature

Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6

Huang, S., Briganti, L., Kvaratskhelia, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

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

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 163.28 kDa 
• Atom Count: 9,980 
• Modelled Residue Count: 1,295 
• Deposited Residue Count: 1,476 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A, B, C, D, E, F	231	Human immunodeficiency virus 1	Mutation(s): 5
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493  Go to UniProtKB:  P12493

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage and polyadenylation specificity factor subunit 6	G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16630 (Homo sapiens) Explore Q16630  Go to UniProtKB:  Q16630
PHAROS:  Q16630 GTEx:  ENSG00000111605

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.347 
• R-Value Work: 0.307 
• R-Value Observed: 0.309 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.172	α = 90
b = 133.172	β = 90
c = 205.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Briganti, L., Schope, L., Kvaratskhelia, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI157802
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI162665

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release