Primary Citation PubMed: 9430589
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Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA.
(2006) Nucleic Acids Res 34
PubMed: 16522643 | PubMedCentral: PMC1390681 | DOI: 10.1093/nar/gkl004
Figure 8 High-resolution structures of ( a ) NC•SL3 (PDB:1A1T) and ( b ) NC•SL2 (PDB:1F6U).
Publication Year: 2006
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
(2007) Nucleic Acids Res 35
PubMed: 17169987 | PubMedCentral: PMC1802613 | DOI: 10.1093/nar/gkl1074
The central panel represents superposition of ab initio models of the free NC domain in solution and of this domain in complex with the oligonucleotide (yellow and grey beads, respectively) and NMR-de... ived models of these constructs (purple and red backbones for first models in the PDB files 1AAF and 1A1T, respectively).
The high-resolution models were retrieved from the Brookhaven Protein Data Bank ( 12 ) (PDB): dUTPase 2AKV, NC domain with oligonucleotide 1A1T, model 1 ( 13 ) and free NC 1AAF, model 1 ( 14 ).
In contrast, NC in complex with oligonucleotide has a much bulkier appearance, larger excluded volume and is well superimposed with the relatively compact atomic model of this complex obtained by NMR (1A1T, 1AAF) ( 30 ).
Publication Year: 2007
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
(2008) PLoS Comput Biol 4
PubMed: 18989394 | PubMedCentral: PMC2566816 | DOI: 10.1371/journal.pcbi.1000214
Thus, the following structures were used: Gag derived proteins: matrix p17, capsid p24, nucleocapsid p7 (PDB IDs: 1tam, 1e6j, 1a1t, respectively); Pol derived proteins: protease p10, reverse transcrip... ase p51, RNase p15, integrase p31 (PDB IDs: 1aaq, 1rtd, 1o1w, 2itg, respectively); Vpr p12/p10 (PDB ID: 1m8l); Tat p16/p14 (PDB ID: 1mnb); Rev p19 (PDB ID: 1etf); Vpu p16 (PDB ID: 1vpu); Env derived proteins: gp120, gp41 (PDB IDs: 1gc1, 1env, respectively); Nef p27/p25 (PDB ID: 2nef).
Publication Year: 2008
Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein.
(2009) Nucleic Acids Res 37
PubMed: 19151084 | PubMedCentral: PMC2647317 | DOI: 10.1093/nar/gkn1083
( 53 , 77 , 76 ) corresponding to PDB structures: 1A1T, 1BJ6, 2EXF, respectively].
Publication Year: 2009
Targeting RNA-protein interactions within the human immunodeficiency virus type 1 lifecycle.
(2013) Biochemistry 52
PubMed: 24358934 | PubMedCentral: PMC3928988 | DOI: 10.1021/bi401270d
The binding of HIV-1 NC protein to the RNA SL3 has been well characterized by 1 H NMR spectroscopy (PDB 1A1T, Figure 3 B).
(B) 3-D model of the HIV-1 nucleocapsid–WT-3 complex (PDB 1A1T) depicting the protein and the RNA hairpin with a green and white ribbon, respectively.
Publication Year: 2013
Dynamics of linker residues modulate the nucleic acid binding properties of the HIV-1 nucleocapsid protein zinc fingers.
(2014) PLoS One 9
PubMed: 25029439 | PubMedCentral: PMC4100767 | DOI: 10.1371/journal.pone.0102150
(a) SL3-NC (pdb 1a1t); (b) PBS-NC (2exf); (c) SL2-NC (1f6u); (d) mini-cTAR-NC (2l4l).
Publication Year: 2014
Functional conservation of HIV-1 Gag: implications for rational drug design.
(2013) Retrovirology 10
PubMed: 24176092 | PubMedCentral: PMC4228425 | DOI: 10.1186/1742-4690-10-126
Figure (C) shows the structural complex of nucleocapsid and RNA (left, PDB: 1A1T) and the structural complex of nucleocapsid and inhibitor CAA (right, PDB: 2M3Z).
A new ensemble coevolution system for detecting HIV-1 protein coevolution.
(2015) Biol Direct 10
PubMed: 25564011 | PubMedCentral: PMC4332441 | DOI: 10.1186/s13062-014-0031-8
The PDB dataset included: 1HIW (matrix), 3H4E (capsid), 1A1T (nucleocapsid), 2C55 (p6) and 1TW7 (protease).
Publication Year: 2015
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