6VRG

Structure of HIV-1 integrase with native amino-terminal sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

Currently 6VRG does not have a validation slider image.


This is version 1.2 of the entry. See complete history


Literature

Influence of the amino-terminal sequence on the structure and function of HIV integrase.

Eilers, G.Gupta, K.Allen, A.Zhou, J.Hwang, Y.Cory, M.B.Bushman, F.D.Van Duyne, G.

(2020) Retrovirology 17: 28-28

  • DOI: https://doi.org/10.1186/s12977-020-00537-x
  • Primary Citation of Related Structures:  
    6VRG

  • PubMed Abstract: 

    Antiretroviral therapy (ART) can mitigate the morbidity and mortality caused by the human immunodeficiency virus (HIV). Successful development of ART can be accelerated by accurate structural and biochemical data on targets and their responses to inhibitors. One important ART target, HIV integrase (IN), has historically been studied in vitro in a modified form adapted to bacterial overexpression, with a methionine or a longer fusion protein sequence at the N-terminus. In contrast, IN present in viral particles is produced by proteolytic cleavage of the Pol polyprotein, which leaves a phenylalanine at the N-terminus (IN 1F). Inspection of available structures suggested that added residues on the N-terminus might disrupt proper protein folding and formation of multimeric complexes.


  • Organizational Affiliation

    Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
A, B, C, D
212Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.919α = 90
b = 102.919β = 90
c = 279.203γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report

Currently 6VRG does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117950
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI126620
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL137063
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129661
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL113252
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS100081
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007632
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI045008

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description