|Entry||Database: PDB / ID: 2kod|
|Title||A high-resolution NMR structure of the dimeric C-terminal domain of HIV-1 CA|
|Components||HIV-1 CA C-terminal domain|
|Keywords||VIRAL PROTEIN / HIV-1 capsid / C-terminal domain|
|Function / homology||Integrase, N-terminal zinc-binding domain / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Reverse transcriptase thumb / Reverse transcriptase connection / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Ribonuclease H domain / Aspartic peptidase, active site / Matrix protein, lentiviral and alpha-retroviral, N-terminal ...Integrase, N-terminal zinc-binding domain / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Reverse transcriptase thumb / Reverse transcriptase connection / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Ribonuclease H domain / Aspartic peptidase, active site / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Zinc finger, CCHC-type / Integrase, catalytic core / Integrase, C-terminal, retroviral / Retroviral nucleocapsid protein Gag / Reverse transcriptase domain / Immunodeficiency lentiviral matrix, N-terminal / Ribonuclease H-like superfamily / Integrase-like, N-terminal / Reverse transcriptase thumb domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase Zinc binding domain / Integrase core domain / gag gene protein p24 (core nucleocapsid protein) / Integrase DNA binding domain / gag gene protein p17 (matrix protein) / Zinc knuckle / Retroviral aspartyl protease / Retropepsins / |RNase H / Zinc finger, CCHC-type superfamily / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Eukaryotic and viral aspartyl proteases active site. / Reverse transcriptase connection domain / Zinc finger CCHC-type profile. / Integrase DNA binding domain profile. / Vpr-mediated nuclear import of PICs / APOBEC3G mediated resistance to HIV-1 infection / Autointegration results in viral DNA circles / Integration of viral DNA into host genomic DNA / Assembly Of The HIV Virion / Binding and entry of HIV virion / 2-LTR circle formation / Plus-strand DNA synthesis / Minus-strand DNA synthesis / Early Phase of HIV Life Cycle / Integration of provirus / Budding and maturation of HIV virion / Uncoating of the HIV Virion / Integrase catalytic domain profile. / Aspartyl protease, retroviral-type family profile. / Zinc finger integrase-type profile. / Reverse transcriptase (RT) catalytic domain profile. / RNase H domain profile. / integrase activity / nuclear transport / viral genome packaging / RNA-dependent DNA biosynthetic process / uncoating of virus / entry into host cell / viral life cycle / induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / HIV-1 retropepsin / virion assembly / retroviral ribonuclease H / exoribonuclease H activity / exoribonuclease H / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase / viral genome integration into host DNA / Nucleotidyltransferases / RNA-directed DNA polymerase activity / suppression by virus of host gene expression / RNA-DNA hybrid ribonuclease activity / fusion of virus membrane with host plasma membrane / establishment of integrated proviral latency / peptidase activity / viral nucleocapsid / lipid binding / DNA recombination / Acting on Ester Bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / DNA binding / zinc ion binding / identical protein binding / Gag-Pol polyprotein|
Function and homology information
|Specimen source||HIV-1 M:B_HXB2R (virus)|
|Method||SOLUTION NMR / simulated annealing|
|Authors||Byeon, I.-J.L. / Jung, J. / Ahn, J. / concel, J. / Gronenborn, A.M.|
|Citation||Journal: Cell / Year: 2009|
Title: Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
Authors: In-Ja L Byeon / Xin Meng / Jinwon Jung / Gongpu Zhao / Ruifeng Yang / Jinwoo Ahn / Jiong Shi / Jason Concel / Christopher Aiken / Peijun Zhang / Angela M Gronenborn
Abstract: Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and ...Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.
SummaryFull reportAbout validation report
|Date||Deposition: Sep 18, 2009 / Release: Nov 24, 2009|
|Structure viewer||Molecule: |
Downloads & links
A: HIV-1 CA C-terminal domain
B: HIV-1 CA C-terminal domain
Mass: 9839.316 Da / Num. of mol.: 2 / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Plasmid name: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt:P04585
|Experiment||Method: SOLUTION NMR|
|sample conditions||Ionic strength: 25 / pH: 6.5 / Pressure: ambient / Temperature: 298 kelvins / Temperature units: K|
|Refinement||Method: simulated annealing / Software ordinal: 1|
Details: The residues 223-231 exhibit unfolded/disordered structure and thus no meaning should be given to the coordinates for these residues.
|NMR representative||Selection criteria: lowest energy|
|NMR ensemble||Conformer selection criteria: structures with the lowest energy|
Conformers calculated total number: 500 / Conformers submitted total number: 30
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