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Unified Data Resource for Cryo-EM [chapter]

Catherine L. Lawson
2010 Methods in Enzymology  
For structures with regular point or helical symmetry, coordinates for one asymmetric unit may be deposited along with transformation matrices to build the assembly (Lawson et al., 2008) .  ...  For structures with regular point or helical symmetry, coordinates are given for the asymmetric unit along with a set of transformation matrices to build the biological assembly (Lawson et al., 2008)  ... 
doi:10.1016/s0076-6879(10)83004-6 pmid:20888470 pmcid:PMC2966391 fatcat:ncsypzwkdvh6dopessk56ubpaq

Comparing cryo-EM structures

Catherine L. Lawson, Wah Chiu
2018 Journal of Structural Biology  
EM Data Bank (EMDB) now holds more than 6500 cryo-EM density maps, and Protein Data Bank (PDB) holds more than 2500 structure coordinates, contributed by the growing cryo-EM community (Patwardhan and Lawson  ...  A total of 66 maps and 142 models were contributed, each with supporting details about the workflow from benchmark to final result ( [dataset] Lawson et al., 2017; [dataset] Lawson et al., 2018) .  ... 
doi:10.1016/j.jsb.2018.10.004 pmid:30321594 pmcid:PMC6464812 fatcat:6ssyvddm55d47gvzkynsuqeb6u

Developing Community Resources for Nucleic Acid Structures

Helen M. Berman, Catherine L. Lawson, Bohdan Schneider
2022 Life  
NtC class BB00 (l acterizes the B form, AA00 (center) A form in both DNA and RNA, and NANT (right) a classified dinucleotides.  ... 
doi:10.3390/life12040540 pmid:35455031 pmcid:PMC9031032 fatcat:2e5nwcxpk5dvdff34brexevwty

The data universe of structural biology

Helen M. Berman, Brinda Vallat, Catherine L. Lawson
2020 IUCrJ  
et al., 2016; Lawson & Chiu, 2018) .  ...  and the National Center for Macromolecular Imaging (NCMI) initiated a collaboration to ensure that data archiving and validation standards for cryo-EM maps and models are coordinated internationally (Lawson  ... 
doi:10.1107/s205225252000562x pmid:32695409 pmcid:PMC7340255 fatcat:mnh7usf2zfg3rljrw77gzy4k4a

Evolving data standards for cryo-EM structures

Catherine L. Lawson, Helen M. Berman, Wah Chiu
2020 Structural Dynamics  
L. Lawson and W. Chiu, J. Struct. Biol. 204(3), 523-526 (2018).  ...  Wah Chiu, Cathy Lawson, Paul Adams First pass analyses of models and data submitted to the 2016 Model Challenge # Year Title/location Organizers Description Key outcomes Model Workshop, CA, USA  ... 
doi:10.1063/1.5138589 pmid:32002441 pmcid:PMC6980868 fatcat:rzpnh3prwfh75fondzo27zjfgy

Letter from the Editorial Team

Thomas L. Brewer, Catherine Langlois, Laura C. Lawson
1999 Journal of International Business Studies  
We are pleased to announce that, effective immediately, new procedures for submission and review of papers are in place for JIBS. We have devised these new procedures to provide an expedited and efficient review process that is author-friendly and reviewer-friendly. The new procedures use electronic files and communications extensively throughout the submission-review process, and we expect them to reduce the turn-aroundtime at several points. We will be reportingthe results of the new procedures in due course.
doi:10.1057/jibs.1999.16 fatcat:vgzml2zewfhgxkpgkomymgipuy

Children's active commuting to school: current knowledge and future directions

Kirsten K Davison, Jessica L Werder, Catherine T Lawson
2008 Preventing Chronic Disease  
Driven largely by international declines in rates of walking and bicycling to school and the noted health benefits of physical activity for children, research on children's active commuting to school has expanded rapidly during the past 5 years. We summarize research on predictors and health consequences of active commuting to school and outline and evaluate programs specific to children's walking and bicycling to school. Literature on children's active commuting to school published before June
more » ... 2007 was compiled by searching PubMed, PsycINFO, and the National Transportation Library databases; conducting Internet searches on program-based activities; and reviewing relevant transportation journals published during the last 4 years. Children who walk or bicycle to school have higher daily levels of physical activity and better cardiovascular fitness than do children who do not actively commute to school. A wide range of predictors of children's active commuting behaviors was identified, including demographic factors, individual and family factors, school factors (including the immediate area surrounding schools), and social and physical environmental factors. Safe Routes to School and the Walking School Bus are 2 public health efforts that promote walking and bicycling to school. Although evaluations of these programs are limited, evidence exists that these activities are viewed positively by key stakeholders and have positive effects on children's active commuting to school. Future efforts to promote walking and bicycling to school will be facilitated by building on current research, combining the strengths of scientific rigor with the predesign and postdesign provided by intervention activities, and disseminating results broadly and rapidly.
pmid:18558018 pmcid:PMC2483568 fatcat:cxcx5ug3irhuxnbbc5ql5drblq

The tryptophan repressor sequence is highly conserved among theEnterobacteriaceae

Dennis N. Arvidson, Cindy Grove Arvidson, Catherine L. Lawson, Jami Miner, Curtis Adams, Philip Youderian
1994 Nucleic Acids Research  
Trp aporepressor binds the corepressor, L-tryptophan, to form a holorepressor complex, which binds trp operator DNA tightly, and inhibits transcription of the tryptophan biosynthetic operon.  ...  Italicized print corresponds to amino acids with side chains involved in binding to corepressor, L-tryptophan.  ...  The other subunit (gray coil) and the two L-typtophan corpressor ligands (gray stick model) are shown for reference.  ... 
doi:10.1093/nar/22.10.1821 pmid:8208606 pmcid:PMC308080 fatcat:v767rzqnpzhg3opyszqjixm5fu

Environment-dependent long-range structural distortion in a temperature-sensitive point mutant

Jannette Carey, Brian Benoff, Balasubramanian Harish, Lara Yuan, Catherine L. Lawson
2011 Protein Science  
Extensive environment-dependent rearrangement of the helix-turn-helix DNA recognition region and adjacent L-tryptophan binding pocket is reported in the crystal structure of dimeric E. coli trp aporepressor  ...  A tris cation occupying one L-tryptophan binding pocket in the L75F apoTrpR structure is also shown (compare dotted surface for tris in (B) and for L-tryptophan in Fig. 1).  ...  In the wt conformer the absence of a sidechain at Gly85 accommodates the L-tryptophan indole 18, 30 ; therefore, L-tryptophan binding would be incompatible with the distorted mutant conformation.  ... 
doi:10.1002/pro.759 pmid:22057811 pmcid:PMC3323781 fatcat:qdvivcoesjgdvbpovftn7axj5i

Structural Investigation ofBorrelia burgdorferiOspB, a BactericidalFab Target

Michael Becker, Jonas Bunikis, Barbara D. Lade, John J. Dunn, Alan G. Barbour, Catherine L. Lawson
2005 Journal of Biological Chemistry  
The OspB-CT crystal form was obtained by mixing 4 l of freshly purified protein with 4 l of 25% PEG550MME, 0.1 M Bicine, 0.1 M sodium bromide, 0.03 M sodium citrate, pH 9.5, and equilibrating at 295 K  ...  Crystals of the OspB-CT ϩ H6831 Fab complex were obtained by mixing 4 l of complex with 4 l of either: (a) 25% PEG 3350, 0.2 M sodium citrate, pH 5.6, (b) 25% PEG 3350, 5% isopropyl alcohol, 0.2 M sodium  ... 
doi:10.1074/jbc.m412842200 pmid:15713683 fatcat:wx3w6olhgvaoriuqdyy6itkdtm

E. coli trp Repressor Forms a Domain-Swapped Array in Aqueous Alcohol

Catherine L Lawson, Brian Benoff, Tatyana Berger, Helen M Berman, Jannette Carey
2004 Structure  
Flexible N-terminal arms mediate surface adjacent to and involving the HTH (Figure 1B) association between dimers bound to tandem DNA (Lawson and Carey, 1993). TrpR dimers also associate sites.  ...  Each subunit is represented as an N and C segment connected by flexible linker L.  ...  Sidechains (labeled) and L-tryptophan (unlabeled) are shown in space-fill. Table 1 .  ... 
doi:10.1016/j.str.2004.03.019 pmid:15274929 pmcid:PMC3228604 fatcat:6dnpgbqtrbc25mtjllhwthyj2m

Structure of theEscherichia coliRNA polymerase α subunit C-terminal domain

Samuel Lara-González, Jens J. Birktoft, Catherine L. Lawson
2010 Acta Crystallographica Section D: Biological Crystallography  
The L-test, based on deviations in local intensities (Padilla & Yeates, 2003) , yielded results that were consistent with pseudomerohedral twinning: |L| = 0.43 (expected value of 0.500 for untwinned and  ...  0.375 for a perfect twin) and L 2 = 0.26 (0.333 for untwinned and 0.200 for a perfect twin).  ... 
doi:10.1107/s0907444910018470 pmid:20606261 pmcid:PMC2897699 fatcat:t2doshpmejelfnzfzyhog2ggve

Representation of viruses in the remediated PDB archive

Catherine L. Lawson, Shuchismita Dutta, John D. Westbrook, Kim Henrick, Helen M. Berman
2008 Acta Crystallographica Section D: Biological Crystallography  
D64, 874-882 Lawson et al. Representation of viruses in the PDB 877 et al. Representation of viruses in the PDB Acta Cryst. (2008). D64, 874-882 Figure 4 et al.  ... 
doi:10.1107/s0907444908017393 pmid:18645236 pmcid:PMC2677383 fatcat:jw6vevz23nghdmc4i66634yqje

Structure of catabolite activator protein with cobalt(II) and sulfate

Ramya R. Rao, Catherine L. Lawson
2014 Acta Crystallographica Section F Structural Biology Communications  
Introduction CAP (catabolite activator protein) is a DNA-binding protein and transcription activator that recruits RNA polymerase to more than 100 genes in Escherichia coli (Busby & Ebright, 1999; Lawson  ...  Activating region 1 (AR1), located on the C-terminal domain, attracts a flexibly tethered RNAP subunit C-terminal domain to bind to a DNA site adjacent to CAP (Benoff et al., 2002; Lawson et al., 2004  ... 
doi:10.1107/s2053230x14005366 pmid:24817710 pmcid:PMC4014319 fatcat:3f6x6mc6q5dbhn2xoglefgf56a
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