UMass Amherst

Welcome to the home page of BMB 695a,
Macromolecular Crystallography (Spring 2009)!

The UMass protein crystallography home page is at

This journal club is organized by Scott Garman, Jeanne Hardy, and Karsten Theis.We share a common interest in structural biology, including X-ray crystallographic techniques. Our labs are all located on the 10th floor of Lederle Tower, along with the X-ray diffraction facility.

If you are looking for the home page of the UMass X-ray diffraction facility, you can find it here.

If you are looking for Karsten Theis' home page, it is here, while Scott Garman's home page is here, and Jeanne Hardy's is here.

Spring 2009 Journal Club Schedule (Biochem 695a, Macromolecular Crystallography):

Journal Club meets Thursdays at 8:20am in 1020 LGRT (Pinkham room). Every week, we will have one discussion leader who will ask for multiple volunteers to present selected data (figures or tables).

Presentation leader
Readings and links
5 Feb 09
AAA ATPase Cassidy paper
Jason M. Davies, Axel T. Brünger, & William I. Weis
"Improved Structures of Full-Length p97, an AAA ATPase: Implications for Mechanisms of Nucleotide-Dependent Conformational Change" Structure (2008) 16:715
12 Feb 09
paper, supplemental
Patrick Scheerer, Jung Hee Park, Peter W. Hildebrand, Yong Ju Kim, Norbert Krauß, Hui-Woog Choe, Klaus Peter Hofmann, & Oliver P. Ernst
"Crystal structure of Opsin in its G-protein-interacting conformation" Nature (2008) 455:497
19 Feb 09
Fe2+ Dioxygenase Nitai paper, supplemental
Elena G. Kovaleva and John D. Lipscomb 
"Crystal Structures of Fe2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product Intermediates" Science (2007) 316:453
26 Feb 09
General discussion Karsten  
Murphy & Theis methods paper  
5 Mar 09
APOBEC Kristen paper, supplemental
Lauren G. Holden, Courtney Prochnow, Y. Paul Chang, Ronda Bransteitter, Linda Chelico,
Udayaditya Sen, Raymond C. Stevens, Myron F. Goodman, & Xiaojiang S. Chen 
"Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications" Nature (2008) 456:121
12 Mar 09
Seneca Valley Virus Nilima paper
Sangita Venkataraman, Seshidhar P. Reddy, Jackie Loo, Neeraja Idamakanti, Paul L. Hallenbeck, and Vijay S. Reddy
 "Structure of Seneca Valley Virus-001: An Oncolytic Picornavirus Representing a New Genus" Structure 16, 1555
Spring Break
26 Mar 09
Complement C3b Sam paper, supplemental (.doc), communication
A. Abdul Ajees, K. Gunasekaran, John E. Volanakis, Sthanam. V. L. Narayana, Girish J. Kotwal & H. M. Krishna Murthy 
"The structure of complement C3b provides insights into complement activation and regulation" Nature (2006) 444:221
2 Apr 09
Aminoacyl-tRNA synthetase Yady paper
Timothy L. Bullock, Annia Rodríguez-Hernández, Eleonora M. Corigliano, and John J. Perona
"A rationally engineered misacylating aminoacyl-tRNA synthetase" PNAS (2008) 105:7428
9 Apr 09
LDL Receptor Nat paper 1, paper 2
Gabby Rudenko, Lisa Henry, Keith Henderson, Konstantin Ichtchenko, Michael S. Brown, Joseph L. Goldstein, Johann Deisenhofer
 "Structure of the LDL Receptor Extracellular Domain at Endosomal pH" Science (2002) 298:2353

Hyock Joo Kwon, Thomas A. Lagace, Markey C. McNutt, Jay D. Horton, and Johann Deisenhofer
"Molecular basis for LDL receptor recognition by PCSK9" PNAS (2008) 105:1820
16 Apr 09
Ube2g2 Ivan paper, supplemental
Wei Li, Daqi Tu, Lianyun Li, Thomas Wollert, Rodolfo Ghirlando, Axel T. Brunger, and Yihong Ye
"Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2" PNAS (2009) 108:3722
23 Apr 09
Mh-p37 methods Melisa paper
Katherine H. Sippel, Arthur H. Robbins, Robbie Reutzel, John Domsic, Susan K. Boehlein, Lakshmanan Govindasamy,
Mavis Agbandje-McKenna, Charles J. Rosserc and Robert McKenna,
"Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37" ActaCryst (2008) D64:1172 
30 Apr 09
classic HLA papers Scott paper1, paper2, N&V
Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, & Wiley DC
"Structure of the human class I histocompatibility antigen, HLA-A2"  Nature (1987) 329:506-512

Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, & Wiley DC
"The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens"
Nature (1987) 329:512-518
7 May 09
In-house sulfur SAD Daniel paper
Jie Nan, Yanfeng Zhou, Cheng Yang, Erik Brostromer, Ole Kristensen, and Xiao-Dong Su
"Structure of a fatty acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation"ActaCryst (2009) D65:440