6JCG

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

Summary for 6JCG

• Entry DOI: 10.2210/pdb6jcg/pdb
• Descriptor: Integrase, CACODYLATE ION (3 entities in total)
• Functional Keywords: hiv, hiv-1, integrase, room temperature, viral protein
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 1
• Total formula weight: 18112.32

Authors

Park, J.H.,Shi, Y.,Han, J.,Li, X.,Kim, T.H.,Yun, J.H. (deposition date: 2019-01-28, release date: 2019-07-17, Last modification date: 2023-11-22)

Primary citation

Park, J.H.,Yun, J.H.,Shi, Y.,Han, J.,Li, X.,Jin, Z.,Kim, T.,Park, J.,Park, S.,Liu, H.,Lee, W.
Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers.
Int J Mol Sci, 20:-, 2019

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.

PubMed: 31010024
DOI: 10.3390/ijms20081943

Experimental method

X-RAY DIFFRACTION (2.5 Å)