Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 18.11 kDa 
• Atom Count: 1118 
• Modelled Residue Count: 141 
• Deposited Residue Count: 163 
• Unique protein chains: 1

6JCG

Room temperature structure of HIV-1 Integrase catalytic core domain by serial femtosecond crystallography.

• PDB DOI: 10.2210/pdb6JCG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-28 Released: 2019-07-17 
• Deposition Author(s): Park, J.H., Shi, Y., Han, J., Li, X., Kim, T.H., Yun, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers.

Park, J.H., Yun, J.H., Shi, Y., Han, J., Li, X., Jin, Z., Kim, T., Park, J., Park, S., Liu, H., Lee, W.

(2019) Int J Mol Sci 20

• PubMed: 31010024 
• DOI: 10.3390/ijms20081943
• Primary Citation of Related Structures:  
  6JCF, 6JCG


• PubMed Abstract: 
  

HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN catalytic core domain at 2.5 Å using microcrystals in XFELs. Compared to the cryogenic structure at 2.1 Å using conventional synchrotron crystallography, there was a good agreement between the two structures, except for a catalytic triad formed by Asp64, Asp116, and Glu152 (DDE) and the lens epithelium-derived growth factor binding sites. The helix III region of the 140-153 residues near the active site and the DDE triad show a higher dynamic profile in the non-cryogenic structure, which is comparable to dynamics data obtained from NMR spectroscopy in solution state.

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Organizational Affiliation: 

Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	163	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	B [auth A], C [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.275	α = 90
b = 73.275	β = 90
c = 66.71	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
CrystFEL	data scaling
Cheetah	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-28 
• Released Date: 2019-07-17 
Deposition Author(s): Park, J.H., Shi, Y., Han, J., Li, X., Kim, T.H., Yun, J.H.

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release