Publications from the Lab

 

Gorelik A, Liu F, Illes K, Nagar B.

J Biol Chem. 2017 Mar 14. pii: jbc.M116.769273. doi: 10.1074/jbc.M116.769273. [Epub ahead of print]

PDB: 5TCD | 5UDY

 

Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations.

Abbas YM, Laudenbach BT, Martínez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):E2106-E2115. doi: 10.1073/pnas.1612444114. Epub 2017 Mar 1.

PDB: 5UDI | 5UDJ | 5UDK | 5UDL

 

Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.

Gorelik A, Heinz LX, Illes K, Superti-Furga G, Nagar B.

J Biol Chem. 2016 Nov 11;291(46):24054-24064. Epub 2016 Sep 28.

PDB: 5KAR | 5KAS

 

Crystal structure of mammalian acid sphingomyelinase.

Gorelik A, Illes K, Heinz LX, Superti-Furga G, Nagar B.

Nat Commun. 2016 Jul 20;7:12196. doi: 10.1038/ncomms12196.

PDB: 5FI9 | 5FIB | 5FIC | 5HQN

 

Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3A.

Gorelik A, Illes K, Superti-Furga G, Nagar B.

J Biol Chem. 2016 Mar 18;291(12):6376-85. doi: 10.1074/jbc.M115.711085. Epub 2016 Jan 20.

PDB: 5FC1 | 5FC5 | 5FC6 | 5FC7 | 5FCA | 5FCB

 

DAP5 associates with eIF2β and eIF4AI to promote Internal Ribosome Entry Site driven translation.

Liberman N, Gandin V, Svitkin YV, David M, Virgili G, Jaramillo M, Holcik M, Nagar B, Kimchi A, Sonenberg N.

Nucleic Acids Res. 2015 Apr 20;43(7):3764-75. doi: 10.1093/nar/gkv205. Epub 2015 Mar 16.

 

An immunogenic peptide in the A-box of HMGB1 protein reverses apoptosis-induced tolerance through RAGE receptor.

LeBlanc PM, Doggett TA, Choi J, Hancock MA, Durocher Y, Frank F, Nagar B, Ferguson TA, Saleh M.

J Biol Chem. 2014 Mar 14;289(11):7777-86. doi: 10.1074/jbc.M113.541474. Epub 2014 Jan 28.

 

Structure of parkin reveals mechanisms for ubiquitin ligase activation.

Trempe JF, Sauvé V, Grenier K, Seirafi M, Tang MY, Ménade M, Al-Abdul-Wahid S, Krett J, Wong K, Kozlov G, Nagar B, Fon EA, Gehring K.

Science. 2013 Jun 21;340(6139):1451-5. doi: 10.1126/science.1237908. Epub 2013 May 9.

PDB: 4K7D | 4K95

 

Structural basis for the recruitment of the human CCR4-NOT deadenylase complex by tristetraprolin.

Fabian MR, Frank F, Rouya C, Siddiqui N, Lai WS, Karetnikov A, Blackshear PJ, Nagar B, Sonenberg N.

Nat Struct Mol Biol. 2013 Jun;20(6):735-9. doi: 10.1038/nsmb.2572. Epub 2013 May 5.

PDB: 4J8S

 

An autoinhibited structure of α-catenin and its implications for vinculin recruitment to adherens junctions.

Ishiyama N, Tanaka N, Abe K, Yang YJ, Abbas YM, Umitsu M, Nagar B, Bueler SA, Rubinstein JL, Takeichi M, Ikura M.

J Biol Chem. 2013 May 31;288(22):15913-25. doi: 10.1074/jbc.M113.453928. Epub 2013 Apr 15.

 

Structural analysis of the DAP5 MIF4G domain and its interaction with eIF4A.

Virgili G, Frank F, Feoktistova K, Sawicki M, Sonenberg N, Fraser CS, Nagar B.

Structure. 2013 Apr 2;21(4):517-27. doi: 10.1016/j.str.2013.01.015. Epub 2013 Mar 7.

PDB: 4IUL

 

Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins.

Abbas YM, Pichlmair A, Górna MW, Superti-Furga G, Nagar B.

Nature. 2013 Feb 7;494(7435):60-4. doi: 10.1038/nature11783. Epub 2013 Jan 13.

PDB: 4HOU | 4HOQ | 4HOR | 4HOS | 4HOT

 

The 5' binding MID domain of human Argonaute2 tolerates chemically modified nucleotide analogues.

Deleavey GF, Frank F, Hassler M, Wisnovsky S, Nagar B, Damha MJ.

Nucleic Acid Ther. 2013 Feb;23(1):81-7. doi: 10.1089/nat.2012.0393. Epub 2013 Jan 5.

 

Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.

Frank F, Hauver J, Sonenberg N, Nagar B.

EMBO J. 2012 Aug 29;31(17):3588-95. doi: 10.1038/emboj.2012.204. Epub 2012 Jul 31.

PDB: 4G0M | 4G0O | 4G0P | 4G0Q | 4G0X | 4G0Y | 4G0Z

 

miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT.

Fabian MR, Cieplak MK, Frank F, Morita M, Green J, Srikumar T, Nagar B, Yamamoto T, Raught B, Duchaine TF, Sonenberg N.

Nat Struct Mol Biol. 2011 Oct 7;18(11):1211-7. doi: 10.1038/nsmb.2149. Erratum in: Nat Struct Mol Biol. 2012 Mar;19(3):364.

 

Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain.

Frank F, Fabian MR, Stepinski J, Jemielity J, Darzynkiewicz E, Sonenberg N, Nagar B.

EMBO Rep. 2011 May;12(5):415-20. doi: 10.1038/embor.2011.48. Epub 2011 Apr 8.

PDB: 3QX8 | 3QX9

 

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2.

Frank F, Sonenberg N, Nagar B.

Nature. 2010 Jun 10;465(7299):818-22. doi: 10.1038/nature09039. Epub 2010 May 26.

PDB: 3LUC | 3LUD | 3LUG | 3LUH | 3LUJ | 3LUK

 

Crystallization and preliminary X-ray diffraction analysis of the MIF4G domain of DAP5.

Frank F, Virgili G, Sonenberg N, Nagar B.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jan 1;66(Pt 1):15-9. doi: 10.1107/S1744309109044315. Epub 2009 Dec 25.

 

Crystallization and preliminary X-ray diffraction analysis of the middle domain of Paip1.

Kanaan AS, Frank F, Maedler-Kron C, Verma K, Sonenberg N, Nagar B.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Oct 1;65(Pt 10):1060-4. doi: 10.1107/S1744309109036513. Epub 2009 Sep 25.

 

Structural Biology in the Battle Against BCR-Abl

Nagar, B.

Expert Opinion on Therapeutic Patents 200 18(9):975-988.

 

c-Abl tyrosine kinase and inhibition by the cancer drug imatinib (Gleevec/STI-571).

Nagar B.

J Nutr. 2007 Jun;137(6 Suppl 1):1518S-1523S; discussion 1548S.

 

Crystal structure of the bb' domains of the protein disulfide isomerase ERp57.

Kozlov G, Maattanen P, Schrag JD, Pollock S, Cygler M, Nagar B, Thomas DY, Gehring K.

Structure. 2006 Aug;14(8):1331-9.

 

 

Publications from Post-doc

 

c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty.

Seeliger MA, Nagar B, Frank F, Cao X, Henderson MN, Kuriyan J.

Structure. 2007 Mar;15(3):299-311.

PDB: 2OIQ

 

Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase.

Nagar B, Hantschel O, Seeliger M, Davies JM, Weis WI, Superti-Furga G, Kuriyan J.

Mol Cell. 2006 Mar 17;21(6):787-98.

PDB: 2FO0

 

Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless.

Sondermann H, Nagar B, Bar-Sagi D, Kuriyan J.

Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16632-7. Epub 2005 Nov 2.

 

SAXS and the working protein.

Nagar B, Kuriyan J.

Structure. 2005 Feb;13(2):169-70.

 

Structural basis for the autoinhibition of c-Abl tyrosine kinase.

Nagar B, Hantschel O, Young MA, Scheffzek K, Veach D, Bornmann W, Clarkson B, Superti-Furga G, Kuriyan J.

Cell. 2003 Mar 21;112(6):859-71.

PDB: 1OPJ | 1OPK | 1OPL

 

A myristoyl/phosphotyrosine switch regulates c-Abl.

Hantschel O, Nagar B, Guettler S, Kretzschmar J, Dorey K, Kuriyan J, Superti-Furga G.

Cell. 2003 Mar 21;112(6):845-57.

 

Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS.

Margarit SM, Sondermann H, Hall BE, Nagar B, Hoelz A, Pirruccello M, Bar-Sagi D, Kuriyan J.

Cell. 2003 Mar 7;112(5):685-95.

PDB: 1NVU | 1NVV | 1NVW | 1NVX

 

Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia.

Shah NP, Nicoll JM, Nagar B, Gorre ME, Paquette RL, Kuriyan J, Sawyers CL.

Cancer Cell. 2002 Aug;2(2):117-25.

 

Characterization of potent inhibitors of the Bcr-Abl and the c-kit receptor tyrosine kinases.

Wisniewski D, Lambek CL, Liu C, Strife A, Veach DR, Nagar B, Young MA, Schindler T, Bornmann WG, Bertino JR, Kuriyan J, Clarkson B.

Cancer Res. 2002 Aug 1;62(15):4244-55.

 

Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571).

Nagar B, Bornmann WG, Pellicena P, Schindler T, Veach DR, Miller WT, Clarkson B, Kuriyan J.

Cancer Res. 2002 Aug 1;62(15):4236-43.

 PDB: 1M52 | 1IEP

 

Publications from PhD

 

X-ray crystal structure of a galactose-specific C-type lectin possessing a novel decameric quaternary structure.

Walker JR, Nagar B, Young NM, Hirama T, Rini JM.

Biochemistry. 2004 Apr 6;43(13):3783-92.

PDB: 1MUQ | 1JZN

 

The functional role of conserved acidic residues of the Qcr7 protein of the cytochrome bc(1) complex in Saccharomyces cerevisiae.

Lee SY, Raha S, Nagar B, Robinson BH.

Arch Biochem Biophys. 2001 Sep 15;393(2):207-14.

 

The use of SnB to determine an anomalous scattering substructure.

Smith GD, Nagar B, Rini JM, Hauptman HA, Blessing RH.

Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):799-804.

 

X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2.

Nagar B, Jones RG, Diefenbach RJ, Isenman DE, Rini JM.

Science. 1998 May 22;280(5367):1277-81.

PDB: 1C3D

 

Structural basis of calcium-induced E-cadherin rigidification and dimerization.

Nagar B, Overduin M, Ikura M, Rini JM.

Nature. 1996 Mar 28;380(6572):360-4.

PDB: 1EDH