Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster

A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700

Rethinking the politics of gender and agency: an encounter with the ‘otherness’ of medieval Japan

This article engages with recent debates within feminism itself to rethink women, gender, body, and agency as conceptual categories for reading medieval Japanese literary/Buddhist texts. It questions the unreflexive transposition of contemporary understandings of concepts to the past, on the grounds that this produces anachronistic readings of the worlds we seek to understand. It argues that in medieval Japanese texts gender did not function as a ‘social’ category posited against the ‘natural’ fact of sex, and that gender was a kind of script and that it was the specificity of the gendered performance, rather than the sexual attributes and reproductive functions of the body, that gave substance to the categories ‘male’ and ‘female.’ The article also offers a critique of contemporary uses of the term agency in analyses of women and Buddhism in medieval Japan, arguing that agency here is defined as something possessed by autonomous individuals with free will, whose natural inclination is to strive to resist against the oppressive conditions of their lives. This modern liberal conception of agency, which is secular in nature, grants agency to humans alone. This anthropocentric view of the world necessitates the evisceration of the agency of gods, buddhas, dreams and material objects, all of whom are central actors in the cosmological/social world of medieval Japan

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB

Association of Ferredoxin:NADP+ oxidoreductase with the photosynthetic apparatus modulates electron transfer in Chlamydomonas reinhardtii

R.M. acknowledges support from the MEXT (Ministry of Education, Culture, Sports, Science and Technology, 15K21122). T.H. gratefully acknowledges support from the DFG (DIP project cooperation “Nanoengineered optoelectronics with biomaterials and bioinspired assemblies”) and the Volkswagen Foundation (LigH2t). G.K. acknowledges support from CREST, Japan Science and Technology Agency. M.H. acknowledges support from the DFG (Deutsche Forschungsgemeinschaft, HI 739/13-1)

Federating structural models and data:Outcomes from a workshop on archiving integrative structures

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here

Community recommendations on cryoEM data archiving and validation

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop’s motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.The workshop was supported by funding to PDBe and EMDB by the Wellcome Trust (grant No. 104948/Z/14/Z awarded to GJK, SV and AP) and by the European Molecular Biology Laboratory. Travel was supported by the PDBe, EMDB, RCSB PDB, PDBj, BMRB and EMDR. RCSB PDB is jointly funded by the National Science Foundation (grant No. DBI1832184); the US Department of Energy (grant No. DESC0019749); and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health (grant No. R01GM133198). PDBj is funded by JST-NBDC and BMRB by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) (grant No. R24GM150793). EMDR was funded by the NIGMS of the NIH (grant No. R01GM079429).Peer reviewe