Structures

PDB: 7RIK, Magic-Angle-Spinning NMR structure of Kinesin-1 motor domain assembled with microtubules (Zhang et al, 2022).
PDB: 7SD4, SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein (Sarkar et al, 2022).
  EMDB-13423, The cryoEM density map hexamer from PFO perforated VLPs in presence of IP6 (Ni et al, 2021). See also EMDB-12454
6xqj

PDB: 6XQJ, Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A (Byeon et al., 2021). See also 6XQI
PDB: 7ASL, HIV-1 Gag immature lattice. GagSP1T8I (Mendonca, et al 2021). See also 7ASH, 7ASL, EMD 12287.
  PDB: 6ZDJ, Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,10) (Ni et al, 2020) See also 6SKK, 6SKM, 6SKN, 6SLQ, 6SLU, 6SMU, 6Y9V, 6Y9W, 6Y9X, 6Y9Y, 6Y9Z, 6YJ5, EMD-11176.

PDB: 6X63, Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR (Lu et al., 2020). See also 6WAP.

EMD-10277, Cryo-EM structure of human SERINC5 in LMNG micelles, bound to Fab.  (Pye et al., 2020)

PDB: 6SP2 CryoEM structure of SERINC from Drosophila melanogaster (Pye et al., 2020). See also EMD-10279
 

EMD-10041, SIVrcm intasome (Cook et al, 2020).     See also: EMDB 10042, 10043, and 10044
 

PDB ID: 6RWL, SIVrcm intasome (Cook et al, 2020).     See also: 6RWM (with bictegravir), 6RWN (with dolutegravir), 6RWO (with INSTI resistance mutations Q148H/G140S in complex with bictegravir).
 

PDB ID: 6OBH Structure of HIV-1 CA 1/2-hexamer (Summers et al, 2019).     See also: 6OMT (R18D hexamer), 6MQA (P207S hexamer),
6MQO (G208R hexamer), 6MQP (T210K hexamer), 6EC2 (1/3-hexamerEE), 6ECN (1/2-hexamerEE-ΔCTD), 6ECO (hexamer-2foldon)
EMD-8986, A 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1. (Himes and Zhang, 2018).
PDB ID: 6GX9, Crystal structure of the TNPO3 - CPSF6 RSLD complex (Jang et al., 2019).
PDB ID: 6OIY, Structure of Escherichia coli bound to dGTP (Barnes et al., 2019). Also see 6OIW and 6OIX.
PDB ID: 6DI7, Vps1 GTPase-BSE fusion complexed with GDP (Varlakhanova et al., 2018). Also see 6DEF and 6DJQ.
EMD-7874, Helical assembly of the fungal dynamin-related Vps1 in the presence of GMPPCP (Varlakhanova et al., 2018).
PDB ID: 5UOT, Cryo-EM structure of the helical assembly of full length MxB (Alvarez et al, 2017). Also see EMDB-8577)
PDB ID: 5UP4, Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM (Wang et al, 2017). Also see EMDB-8582.
EMD-8582, Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM (Wang et al, 2017). Also see PDB ID: 5UP4.
  PDB ID: 5MLU, Crystal structure of the PFV GAG CBS bound to a mononucleosome (Lesbats et al, 2017). Also see NCBI GEO entry GSE97973
  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
  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: 4QFY, 4QFZ, 4QG0, 4QG1, 4QG2, 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

Plasmids have been deposited at Addgene, including pSICO-CPSF6-358-eGFP (plasmid #11063) and pSICO-CPSF6-358-iRFP670 (plasmid #110694).

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 

The pulse sequences used in our solid-state NMR spectroscopy studies are routinely released to Bruker, to be made available for use by the public.

  • (19)F Dynamic nuclear polarization at fast magic angle spinning for NMR of HIV-1 capsid protein assemblies. (2019) Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. J Am Chem Soc.   141(14):5681-5691. PubMed
  • Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. (2019) Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. J Biomol NMR. 2019 Mar 7. doi: 10.1007/s10858-019-00233-9. PubMed
  • Fast magic angle spinning ¹⁹F NMR of HIV-1 capsid protein assemblies. (2018) Wang M, Lu M, Fritz M, Quinn C, Byeon IJ, Byeon CH, Struppe J, Maas W, Gronenborn A, Polenova T. Angew Chem Int Ed Engl. 57(50):16375-16379. PubMed
  • All-atom virus simulations. (2018) Hadden JA and Perilla JR. Curr Opin Virol. 31:82-91. PubMed
  • (19)F Magic angle spinning NMR spectroscopy and density functional theory calculations of fluorosubstituted tryptophans: Integrating experiment and theory for accurate determination of chemical shift tensors. (2018) Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova, T. J Phys Chem B 122(23):6148-6155. PMC6203958 PubMed
  • emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. (2018) Himes B, Zhang P. Nat Methods. 15(11):955-961. PMC6281437 PubMed
  • 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
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