Nature Structural & Molecular Biology - Issue - nature.com science feeds Nature Structural & Molecular Biology is an integrated forum for structural and molecular studies. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. http://www.nature.com/nsmb/current_issue/ Nature Publishing Group en © 2012 Nature Publishing Group Nature Structural & Molecular Biology 1545-9993 1545-9985 © 2012 Nature Publishing Group permissions@nature.com Nature Structural & Molecular Biology http://www.nature.com/includes/rj_globnavimages/nsmb_logo.gif http://www.nature.com/nsmb/ Enforcing silencing: dynamic HP1 complexes in Neurospora http://feeds.nature.com/~r/nsmb/rss/current/~3/ieHqlzHdXQU/nsmb.2291 Enforcing silencing: dynamic HP1 complexes in Neurospora

Nature Structural & Molecular Biology 19, 465 (2012). doi:10.1038/nsmb.2291

Authors: Lori L Wallrath & Sarah C R Elgin

]]> Enforcing silencing: dynamic HP1 complexes in Neurospora Lori L Wallrath Sarah C R Elgin doi:10.1038/nsmb.2291 Nature Structural & Molecular Biology 19, 465 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2291 http://dx.doi.org/10.1038/nsmb.2291 19 5 News and Views 465 467 http://dx.doi.org/10.1038/nsmb.2291 Dynein dynamics http://feeds.nature.com/~r/nsmb/rss/current/~3/nX-nFuSr3jg/nsmb.2290 Dynein dynamics

Nature Structural & Molecular Biology 19, 467 (2012). doi:10.1038/nsmb.2290

Authors: Peter Höök & Richard Vallee

]]> Dynein dynamics Peter Höök Richard Vallee doi:10.1038/nsmb.2290 Nature Structural & Molecular Biology 19, 467 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2290 http://dx.doi.org/10.1038/nsmb.2290 19 5 News and Views 467 469 http://dx.doi.org/10.1038/nsmb.2290 Understanding decoding http://feeds.nature.com/~r/nsmb/rss/current/~3/5xQAZJDOA9s/nsmb.2297 Understanding decoding

Nature Structural & Molecular Biology 19, 470 (2012). doi:10.1038/nsmb.2297

Author: Arianne Heinrichs

]]> Understanding decoding Arianne Heinrichs doi:10.1038/nsmb.2297 Nature Structural & Molecular Biology 19, 470 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2297 http://dx.doi.org/10.1038/nsmb.2297 19 5 Research Highlights 470 470 http://dx.doi.org/10.1038/nsmb.2297 Small RNA-mediated DNA repair http://feeds.nature.com/~r/nsmb/rss/current/~3/ywassRzsf98/nsmb.2298 Small RNA-mediated DNA repair

Nature Structural & Molecular Biology 19, 470 (2012). doi:10.1038/nsmb.2298

Author: Steve Mason

]]> Small RNA-mediated DNA repair Steve Mason doi:10.1038/nsmb.2298 Nature Structural & Molecular Biology 19, 470 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2298 http://dx.doi.org/10.1038/nsmb.2298 19 5 Research Highlights 470 470 http://dx.doi.org/10.1038/nsmb.2298 Un-arrested development http://feeds.nature.com/~r/nsmb/rss/current/~3/FXQ_biSSFVU/nsmb.2299 Un-arrested development

Nature Structural & Molecular Biology 19, 470 (2012). doi:10.1038/nsmb.2299

Author: Joshua M. Finkelstein

]]> Un-arrested development Joshua M. Finkelstein doi:10.1038/nsmb.2299 Nature Structural & Molecular Biology 19, 470 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2299 http://dx.doi.org/10.1038/nsmb.2299 19 5 Research Highlights 470 470 http://dx.doi.org/10.1038/nsmb.2299 Mad1 attachment http://feeds.nature.com/~r/nsmb/rss/current/~3/bIPZ0x1hcUk/nsmb.2300 Mad1 attachment

Nature Structural & Molecular Biology 19, 470 (2012). doi:10.1038/nsmb.2300

Author: Michelle Montoya

]]> Mad1 attachment Michelle Montoya doi:10.1038/nsmb.2300 Nature Structural & Molecular Biology 19, 470 (2012) 2012-05-03 Nature Structural & Molecular Biology 2012-05-03 10.1038/nsmb.2300 http://dx.doi.org/10.1038/nsmb.2300 19 5 Research Highlights 470 470 http://dx.doi.org/10.1038/nsmb.2300 Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation http://feeds.nature.com/~r/nsmb/rss/current/~3/shIq8K7E5J0/nsmb.2274 Methylated histone H3 Lys9 is a hallmark of heterochromatin, and directs DNA methylation via a complex containing heterochromatin protein 1 (HP1) and a DNA methyltransferase. Genetic and biochemical studies in Neurospora now identify a distinct HP1 complex containing a histone deacetylase that is required for silencing independently of DNA methylation, suggesting that distinct HP1 complexes function in parallel to assemble silent heterochromatin. Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation

Nature Structural & Molecular Biology 19, 471 (2012). doi:10.1038/nsmb.2274

Authors: Shinji Honda, Zachary A Lewis, Kenji Shimada, Wolfgang Fischle, Ragna Sack & Eric U Selker

]]> Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation Shinji Honda Zachary A Lewis Kenji Shimada Wolfgang Fischle Ragna Sack Eric U Selker doi:10.1038/nsmb.2274 Nature Structural & Molecular Biology 19, 471 (2012) 2012-04-15 Nature Structural & Molecular Biology 2012-04-15 10.1038/nsmb.2274 http://dx.doi.org/10.1038/nsmb.2274 19 5 Article 471 477 http://dx.doi.org/10.1038/nsmb.2274 p53-mediated heterochromatin reorganization regulates its cell fate decisions http://feeds.nature.com/~r/nsmb/rss/current/~3/3tUxxTqOPwA/nsmb.2271 SUV39H1 is a histone methyltransferase responsible for the repressive H3K9me3 mark. New data indicate that SUV39H1, via p21, is a target of p53 repression, leading to decreased H3K9me3 levels at p53 promoters and facilitating p53 activation of its target genes. p53-mediated heterochromatin reorganization regulates its cell fate decisions

Nature Structural & Molecular Biology 19, 478 (2012). doi:10.1038/nsmb.2271

Authors: Sathish Kumar Mungamuri, Erica Kay Benson, Shaomeng Wang, Wei Gu, Sam W Lee & Stuart A Aaronson

]]> p53-mediated heterochromatin reorganization regulates its cell fate decisions Sathish Kumar Mungamuri Erica Kay Benson Shaomeng Wang Wei Gu Sam W Lee Stuart A Aaronson doi:10.1038/nsmb.2271 Nature Structural & Molecular Biology 19, 478 (2012) 2012-04-01 Nature Structural & Molecular Biology 2012-04-01 10.1038/nsmb.2271 http://dx.doi.org/10.1038/nsmb.2271 19 5 Article 478 484 http://dx.doi.org/10.1038/nsmb.2271 Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation http://feeds.nature.com/~r/nsmb/rss/current/~3/DDfer7BZbtc/nsmb.2284 The membrane-embedded c-ring allows the passage of protons to power the synthesis of ATP by the FoF1 ATPase. Previous structural data have shown the proton acceptor-donor sites in a closed, ion-locked conformation. Structural and computational data now reveal the open conformation of the yeast mitochondrial c10 ring. Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation

Nature Structural & Molecular Biology 19, 485 (2012). doi:10.1038/nsmb.2284

Authors: Jindrich Symersky, Vijayakanth Pagadala, Daniel Osowski, Alexander Krah, Thomas Meier, José D Faraldo-Gómez & David M Mueller

]]> Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation Jindrich Symersky Vijayakanth Pagadala Daniel Osowski Alexander Krah Thomas Meier José D Faraldo-Gómez David M Mueller doi:10.1038/nsmb.2284 Nature Structural & Molecular Biology 19, 485 (2012) 2012-04-15 Nature Structural & Molecular Biology 2012-04-15 10.1038/nsmb.2284 http://dx.doi.org/10.1038/nsmb.2284 19 5 Article 485 491 http://dx.doi.org/10.1038/nsmb.2284 Insights into dynein motor domain function from a 3.3-Å crystal structure http://feeds.nature.com/~r/nsmb/rss/current/~3/RSa_drX78C4/nsmb.2272 Dynein is a molecular motor involved in many cellular functions. The motor domain of dynein contains six AAA+ domains forming a ring that interacts with the motile linker domain. The structure of yeast dynein motor domain crystallized without nucleotides is now presented at 3.3-Å resolution and shows the specific contacts between linker and ring, with nucleotide interactions at the different AAA+ domains revealed by soaking experiments. Insights into dynein motor domain function from a 3.3-Å crystal structure

Nature Structural & Molecular Biology 19, 492 (2012). doi:10.1038/nsmb.2272

Authors: Helgo Schmidt, Emma S Gleave & Andrew P Carter

]]> Insights into dynein motor domain function from a 3.3-Å crystal structure Helgo Schmidt Emma S Gleave Andrew P Carter doi:10.1038/nsmb.2272 Nature Structural & Molecular Biology 19, 492 (2012) 2012-03-14 Nature Structural & Molecular Biology 2012-03-14 10.1038/nsmb.2272 http://dx.doi.org/10.1038/nsmb.2272 19 5 Article 492 497 http://dx.doi.org/10.1038/nsmb.2272 The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end http://feeds.nature.com/~r/nsmb/rss/current/~3/vLdTCRlJsz8/nsmb.2287 The nonsense-mediated mRNA decay (NMD) pathway is triggered upon assembly of the UPF surveillance complex near an exon junction complex (EJC). Cryo-EM studies have revealed the geometry of this transient assembly between the UPF complex and the EJC, which demonstrates how the UPF1 subunit elicits its RNA helicase activity toward the 3A end of the mRNA. The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end

Nature Structural & Molecular Biology 19, 498 (2012). doi:10.1038/nsmb.2287

Authors: Roberto Melero, Gretel Buchwald, Raquel Castaño, Monika Raabe, David Gil, Melisa Lázaro, Henning Urlaub, Elena Conti & Oscar Llorca

]]> The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end Roberto Melero Gretel Buchwald Raquel Castaño Monika Raabe David Gil Melisa Lázaro Henning Urlaub Elena Conti Oscar Llorca doi:10.1038/nsmb.2287 Nature Structural & Molecular Biology 19, 498 (2012) 2012-04-22 Nature Structural & Molecular Biology 2012-04-22 10.1038/nsmb.2287 http://dx.doi.org/10.1038/nsmb.2287 19 5 Article 498 505 http://dx.doi.org/10.1038/nsmb.2287 Discovery of an archetypal protein transport system in bacterial outer membranes http://feeds.nature.com/~r/nsmb/rss/current/~3/q_OPw0do4oA/nsmb.2261 Bacterial secretion systems are key to pathogenesis, as they secrete the many virulence factors needed for host colonization. Bioinformatic and functional analyses have identified a transport and assembly module (TAM) in proteobacteria that may be necessary for biogenesis of the autotransporter family of virulence factors. Discovery of an archetypal protein transport system in bacterial outer membranes

Nature Structural & Molecular Biology 19, 506 (2012). doi:10.1038/nsmb.2261

Authors: Joel Selkrig, Khedidja Mosbahi, Chaille T Webb, Matthew J Belousoff, Andrew J Perry, Timothy J Wells, Faye Morris, Denisse L Leyton, Makrina Totsika, Minh-Duy Phan, Nermin Celik, Michelle Kelly, Clare Oates, Elizabeth L Hartland, Roy M Robins-Browne, Sri Harsha Ramarathinam, Anthony W Purcell, Mark A Schembri, Richard A Strugnell, Ian R Henderson, Daniel Walker & Trevor Lithgow

]]> Discovery of an archetypal protein transport system in bacterial outer membranes Joel Selkrig Khedidja Mosbahi Chaille T Webb Matthew J Belousoff Andrew J Perry Timothy J Wells Faye Morris Denisse L Leyton Makrina Totsika Minh-Duy Phan Nermin Celik Michelle Kelly Clare Oates Elizabeth L Hartland Roy M Robins-Browne Sri Harsha Ramarathinam Anthony W Purcell Mark A Schembri Richard A Strugnell Ian R Henderson Daniel Walker Trevor Lithgow doi:10.1038/nsmb.2261 Nature Structural & Molecular Biology 19, 506 (2012) 2012-04-01 Nature Structural & Molecular Biology 2012-04-01 10.1038/nsmb.2261 http://dx.doi.org/10.1038/nsmb.2261 19 5 Article 506 510 http://dx.doi.org/10.1038/nsmb.2261 NEDD8 links cullin-RING ubiquitin ligase function to the p97 pathway http://feeds.nature.com/~r/nsmb/rss/current/~3/EFhuI8IIlWU/nsmb.2269 The AAA+ protein p97 and its UBA-UBX cofactors are thought to promote degradation by separating ubiquitinated proteins from membranes or protein complexes. UBA-UBX proteins can interact with cullin-RING ubiquitin ligases, and UBXD7 is now seen to specifically bind NEDD8 on active, neddylated cullins, promoting degradation of a Cul3 substrate. NEDD8 links cullin-RING ubiquitin ligase function to the p97 pathway

Nature Structural & Molecular Biology 19, 511 (2012). doi:10.1038/nsmb.2269

Authors: Willem den Besten, Rati Verma, Gary Kleiger, Robert S Oania & Raymond J Deshaies

]]> NEDD8 links cullin-RING ubiquitin ligase function to the p97 pathway Willem den Besten Rati Verma Gary Kleiger Robert S Oania Raymond J Deshaies doi:10.1038/nsmb.2269 Nature Structural & Molecular Biology 19, 511 (2012) 2012-04-01 Nature Structural & Molecular Biology 2012-04-01 10.1038/nsmb.2269 http://dx.doi.org/10.1038/nsmb.2269 19 5 Article 511 516 http://dx.doi.org/10.1038/nsmb.2269 Human prion protein binds Argonaute and promotes accumulation of microRNA effector complexes http://feeds.nature.com/~r/nsmb/rss/current/~3/MbY97PRZ9IA/nsmb.2273 The association of Argonaute (Ago) proteins with endomembranes is thought to be important for their function. New analyses now demonstrate that a transmembrane form of human prion protein binds Ago through GW-motif-containing octarepeat domains and promotes the accumulation of miRISC effector complexes, thereby mediating effective repression of miRNA targets. Human prion protein binds Argonaute and promotes accumulation of microRNA effector complexes

Nature Structural & Molecular Biology 19, 517 (2012). doi:10.1038/nsmb.2273

Authors: Derrick Gibbings, Pascal Leblanc, Florence Jay, Dominique Pontier, Fabrice Michel, Yannick Schwab, Sandrine Alais, Thierry Lagrange & Olivier Voinnet

]]> Human prion protein binds Argonaute and promotes accumulation of microRNA effector complexes Derrick Gibbings Pascal Leblanc Florence Jay Dominique Pontier Fabrice Michel Yannick Schwab Sandrine Alais Thierry Lagrange Olivier Voinnet doi:10.1038/nsmb.2273 Nature Structural & Molecular Biology 19, 517 (2012) 2012-04-08 Nature Structural & Molecular Biology 2012-04-08 10.1038/nsmb.2273 http://dx.doi.org/10.1038/nsmb.2273 19 5 Article 517 524 http://dx.doi.org/10.1038/nsmb.2273 Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H+/Cl− exchanger http://feeds.nature.com/~r/nsmb/rss/current/~3/Aeru4MrijOE/nsmb.2277 Mechanistic studies of active exchangers suggest that substrate binding in active exchangers is antagonistic, and coupling is maintained by preventing shuttling of the empty transporter. However, isothermal titration calorimetry and free energy calculations now show that substrate binding of H+ and Cl− to the prokaryotic CLC-ec1 exchanger is synergistic and occurs simultaneously. Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H+/Cl− exchanger

Nature Structural & Molecular Biology 19, 525 (2012). doi:10.1038/nsmb.2277

Authors: Alessandra Picollo, Yanyan Xu, Niklaus Johner, Simon Bernèche & Alessio Accardi

]]> Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H+/Cl− exchanger Alessandra Picollo Yanyan Xu Niklaus Johner Simon Bernèche Alessio Accardi doi:10.1038/nsmb.2277 Nature Structural & Molecular Biology 19, 525 (2012) 2012-04-08 Nature Structural & Molecular Biology 2012-04-08 10.1038/nsmb.2277 http://dx.doi.org/10.1038/nsmb.2277 19 5 Article 525 531 http://dx.doi.org/10.1038/nsmb.2277 Antidiabetic phospholipid–nuclear receptor complex reveals the mechanism for phospholipid-driven gene regulation http://feeds.nature.com/~r/nsmb/rss/current/~3/bjHJRxwd0R0/nsmb.2279 Liver receptor homolog 1 (LHR-1) is a nuclear receptor involved in development, lipid homeostasis and metabolism. The crystal structures of the LHR-1 ligand-binding domain in its apo state and in complex with the phospholipid DLPC are now presented. The data, along with biophysical and functional analyses, reveal the highly dynamic nature of the apo receptor and show how DLPC binding affects co-regulator selectivity. Antidiabetic phospholipid–nuclear receptor complex reveals the mechanism for phospholipid-driven gene regulation

Nature Structural & Molecular Biology 19, 532 (2012). doi:10.1038/nsmb.2279

Authors: Paul M Musille, Manish C Pathak, Janelle L Lauer, William H Hudson, Patrick R Griffin & Eric A Ortlund

]]> Antidiabetic phospholipid–nuclear receptor complex reveals the mechanism for phospholipid-driven gene regulation Paul M Musille Manish C Pathak Janelle L Lauer William H Hudson Patrick R Griffin Eric A Ortlund doi:10.1038/nsmb.2279 Nature Structural & Molecular Biology 19, 532 (2012) 2012-04-15 Nature Structural & Molecular Biology 2012-04-15 10.1038/nsmb.2279 http://dx.doi.org/10.1038/nsmb.2279 19 5 Article 532 537 http://dx.doi.org/10.1038/nsmb.2279 ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA http://feeds.nature.com/~r/nsmb/rss/current/~3/biqhNFsea3w/nsmb.2278 Bacterial DNA gyrase uses the energy from ATP to introduce negative supercoils into DNA via formation of a chiral wrap intermediate. Now DNA rotation and contraction are simultaneously visualized using a single-molecule setup. The data reveal multiple steps, including a dominant non-chiral intermediate step. ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA

Nature Structural & Molecular Biology 19, 538 (2012). doi:10.1038/nsmb.2278

Authors: Aakash Basu, Allyn J Schoeffler, James M Berger & Zev Bryant

]]> ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA Aakash Basu Allyn J Schoeffler James M Berger Zev Bryant doi:10.1038/nsmb.2278 Nature Structural & Molecular Biology 19, 538 (2012) 2012-04-08 Nature Structural & Molecular Biology 2012-04-08 10.1038/nsmb.2278 http://dx.doi.org/10.1038/nsmb.2278 19 5 Article 538 546 http://dx.doi.org/10.1038/nsmb.2278 Rapid oligomer formation of human muscle acylphosphatase induced by heparan sulfate http://feeds.nature.com/~r/nsmb/rss/current/~3/hNds349tMU8/nsmb.2286 Heparan sulfate can promote formation of amyloid fibrils by different proteins. The early steps and kinetics of this process are now studied in detail, using a stopped-flow setup and the protein mAcP. The data and analysis reveal two steps, binding of mAcP to heparan sulfate and conversion to a misfolded state, followed by aggregation of the heparan sulfate–bound proteins. Rapid oligomer formation of human muscle acylphosphatase induced by heparan sulfate

Nature Structural & Molecular Biology 19, 547 (2012). doi:10.1038/nsmb.2286

Authors: Neda Motamedi-Shad, Tommaso Garfagnini, Amanda Penco, Annalisa Relini, Federico Fogolari, Alessandra Corazza, Gennaro Esposito, Francesco Bemporad & Fabrizio Chiti

]]> Rapid oligomer formation of human muscle acylphosphatase induced by heparan sulfate Neda Motamedi-Shad Tommaso Garfagnini Amanda Penco Annalisa Relini Federico Fogolari Alessandra Corazza Gennaro Esposito Francesco Bemporad Fabrizio Chiti doi:10.1038/nsmb.2286 Nature Structural & Molecular Biology 19, 547 (2012) 2012-04-22 Nature Structural & Molecular Biology 2012-04-22 10.1038/nsmb.2286 http://dx.doi.org/10.1038/nsmb.2286 19 5 Article 547 554 http://dx.doi.org/10.1038/nsmb.2286 Crystal structure of a group II intron in the pre-catalytic state http://feeds.nature.com/~r/nsmb/rss/current/~3/zNug4gMUdv4/nsmb.2270 Group II introns, which are self-splicing catalytic RNAs, catalyze splicing in two distinct steps. The crystal structure of a group II intron in the pre-catalytic state directly preceding the first splicing step reveals a sharp kink in the backbone that presents the scissile phosphate of the splice site to the active site. Crystal structure of a group II intron in the pre-catalytic state

Nature Structural & Molecular Biology 19, 555 (2012). doi:10.1038/nsmb.2270

Authors: Russell T Chan, Aaron R Robart, Kanagalaghatta R Rajashankar, Anna Marie Pyle & Navtej Toor

Group II introns are self-splicing catalytic RNAs that are thought to be ancestral to the spliceosome. Here we report the 3.65-Å crystal structure of the group II intron from Oceanobacillus iheyensis in the pre-catalytic state. The structure reveals the conformation of the 5′ splice site in the catalytic core and represents the first structure of an intron prior to the first step of splicing.

]]> Crystal structure of a group II intron in the pre-catalytic state Russell T Chan Aaron R Robart Kanagalaghatta R Rajashankar Anna Marie Pyle Navtej Toor doi:10.1038/nsmb.2270 Nature Structural & Molecular Biology 19, 555 (2012) 2012-04-08 Nature Structural & Molecular Biology 2012-04-08 10.1038/nsmb.2270 http://dx.doi.org/10.1038/nsmb.2270 19 5 Brief Communication 555 557 http://dx.doi.org/10.1038/nsmb.2270