Structures

  PDB ID: 5MOR, Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex (Ballandras-Colas et al, 2017). Also see: 5LLJ, 5M0Q, 5T3A, and EMD-4138
  EMDB: EMD-8404, Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs (Ning et al, 2016). Also see: EMD-8403
  PDB ID: 5T82, HIV-1 reverse transcriptase thumb subdomain (Sharaf et al, 2016). Also see: BioMagResBank entry 30171
  PDB ID: 5JK7, The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex (Wu et al, 2016).
  PDB ID: 2NBQ, NMR Structure of the C-Terminal Domain of human APOBEC3B (Byeon et al, 2016). Also see: BioMagResBank entry 25985
  PDB ID: 5CZ2, Crystal structure of a two-domain fragment of MMTV integrase (Ballandras-Colas et al, 2016). Also see: 5CZ1 and 5D7U.
  PDB ID: 5FJB, Cyclophilin A Stabilize HIV-1 Capsid through a novel non- canonical binding site (Liu et al, 2016). Also see: EMDB-3075.
PDB ID: 4Z8L, Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex (Wu et al, 2015)
PDB ID: 4U5W, Crystal structure of HIV-1 Nef-SF2 core domain in complex with the Src family kinase Hck SH3-SH2 tandem regulatory domains (Alvarado et al, 2014)

PDB ID: 4QFX, Crystal structure of the tetrameric dGTP/dATP-bound SAMHD1 (RN206) mutant catalytic core (Koharudin et al, 2014). Also see: 4QFY4QFZ4QG04QG14QG2, and 4QG4.

PDB ID: 4WHJ, Myxovirus Resistance Protein 2 (MxB) (Fribourgh et al, 2014)
PDB ID: 4C0Q, Transportin 3 in complex with Ran(Q69L)GTP (Maertens et al, 2014)
PDB ID: 4C0P, Unliganded Transportin 3 (Maertens et al, 2014)
PDB ID: 4C0O, Transportin 3 in complex with phosphorylated ASF/SF2(Maertens et al, 2014)
PDB ID: 4BZC, Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core (Ji et al, 2013)
4BZB PDB ID: 4BZB, Crystal structure of the tetrameric dGTP-bound SAMHD1 mutant catalytic core (Ji et al, 2013)
PDB ID: 3J3Q, Atomic-level structure of the entire HIV-1 capsid (Zhao et al, 2013)
PDB ID: 3J3Y, Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers) (Zhao et al, 2013)
PDB ID: 3J34,  Structure of HIV-1 Capsid Protein by Cryo-EM (Zhao et al, 2013)
EMDB Entry: EMD-5582, Cryo-EM structure of HIV-1 capsid assembly (Zhao et al, 2013)
EMDB Entry: EMD-5639, Cryo-electron tomography reconstruction of native HIV-1 core (Zhao et al, 2013)

EMDB Entry: EMD-5523, Reconstruction of CA in HIV-1 CA-SP1-NC assembly (Meng et al, 2012)

PDB ID: 2M65, NMR structure of human restriction factor APOBEC3A (Byeon et al, 2013)
PDB 4e5z PDB ID: 4e5z, Crystal structure of DNA damage-binding protein 1 with DNA (Yeh et al, 2012)
PDB ID: 4B3N,Crystal structure of rhesus TRIM5alpha PRY/SPRY domain (Yang et al, 2012)
 PDB ID: 3NTE,Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein (Du et al, 2010)
PDB ID: 2KOD, Solution NMR structure of dimeric HIV-1 capsid protein C-terminal domain (Byeon et al, 2009)
PDB ID: 3NHN, Crystal structure of Hck regulatory region (Alvarado et al, 2010)
EMDB Entry: EMD-5136, cryoEM map of HIV-1 capsid in a helical tubular assembly (Byeon et al, 2009)

     

Predictions

The mission of the Data Integration and Bioinformatics Core during Years 1-3 was to develop algorithms that predict and rank interactions between HIV-1 proteins and cellular proteins. In year 4, the prediction model was significantly improved by inclusion of additional data points. HIV PPI Model Predictions are available through our sister center (the HARC) via their online tool: GPS-PROT at http://www.gpsprot.org/ After entering the site, choose "PCHPI Pred" under the HIV-Human PPIs heading.

Also See:

*Refining literature curated protein interactions using expert opinions. Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J. (2015) Pac Symp Biocomput. 2015:318-29. PubMed

*Prediction of interactions between HIV-1 and human proteins by information integration.Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J. (2009) Pac Symp Biocomput. 2009:516-27.  PubMed

*Alternative paths in HIV-1 targeted human signal transduction pathways.Balakrishnan S, Tastan O, Carbonell J, Klein-Seetharaman J (2009) BMC Genomics 10 Suppl 3:S30. NCBI Free Text 

Proteins and Expression Protocols

HIV-1 CA proteins (cDNA from the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, Erickson-Viitanen, S. et al., AIDS Res Hum Retroviruses 5, 577-591, 1989).

HIV-1 consensus Nef (cDNA from the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID NIH, Anderson, S. et al., J. Virol. 67, 4923-4931, 1993).

For clones and detailed purification protocols, please contact This email address is being protected from spambots. You need JavaScript enabled to view it.

Experimental Protocols 

*Transmission electron microscopy for the evaluation and optimization of crystal growth. Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. (2016) Acta Crystallogr D Struct Biol. 72(Pt 5):603-15. PMC4854312  PubMed

*Click labeling of unnatural sugars metabolically incorporated into viral envelope glycoproteins enables visualization of single particle fusion. Oum YH, Desai TM, Marin M, Melikyan GB.  (2016) J Virol Methods 233:62-71. PubMed

*Dynamic nuclear polarization enhanced MAS NMR for structural analysis of HIV-1 protein assemblies. Gupta R, Lu M, Hou G, Caporini MA, Rosay M, Maas WE, Struppe JO, Suiter CL, Ahn J, Byeon IL, Franks WT, Orwick-Rydmark M, Bertarello A, Oschkinat H, Lesage A, Pintacuda G, Gronenborn AM, Polenova TE. (2016) J Phys Chem B 120(2):329-39. PMC4890707 PubMed

*Tubular crystals and helical arrays: structural determination of HIV-1 capsid assemblies using Iterative Helical Real-Space Reconstruction. Zhang P., Meng X. and Zhao G. (2013) Methods Mol Biol 955:381-99. PubMed 

*Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. Strunk KM, Wang K, Ke D, Gray JL, Zhang P. (2012) J Microsc. 247(3): 220  PubMed

*Enhanced sensitivity by nonuniform sampling enables multidimensional MAS NMR spectroscopy of protein assemblies. Paramasivam S, Suiter CL, Hou G, Sun S, Palmer M, Hoch JC, Rovnyak D, Polenova T. (2012) J Phys Chem B. 116(25): 7416 PubMed

*Solid-State NMR spectroscopy of Protein Complexes. Sun S, Paramasivam S, Yan S, Han Y, Lightcap C, Williams JC, Byeon IL, Ahn J, Gronenborn AM, Polenova T. (2012, 831: 303-31) In “Protein NMR Techniques”, “Methods in Molecular Biology” book series, Eds. A. Shekhtman and D. Burz, Humana Press. PubMed

*3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. Wang K, Strunk K, Zhao G, Gray JL, Zhang P. (2012) J Struct Biol.  PubMed

*CryoEM analysis of HIV-1 capsid assembly and structural consequences of TRIM5α binding. Zhao G and Zhang P. (2012) In "Human Retroviruses: Methods and Protocols" In Press.

*Solid-State NMR spectroscopy of Protein Complexes. Sun S, Paramasivam S, Yan S, Han Y, Lightcap C, Williams JC, Byeon IL, Ahn J, Gronenborn AM, Polenova T. (2012, 831: 303-31) In “Protein NMR Techniques”, “Methods in Molecular Biology” book series, Eds. A. Shekhtman and D. Burz, Humana Press. PubMed

*Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-Space Reconstruction. Meng X, Zhao G, and Zhang P. (2011) Journal of Visualized Experiments (54) Free Text

Joomla Template: from JoomlaShack