Community recommendations on cryoEM data archiving and validation

Authors: Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Catherine L. Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H. W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar

Source: IUCrJ, Vol 11, Iss 2, Pp 140-151 (2024)

Subject Terms: cryogenic-specimen electron microscopy, data archiving, validation, quality control, electron microscopy data bank, protein data bank, single-particle cryoem, databases, bioinformatics, structure determination, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252524001246; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/0e43f020fe4a4894b6f5aa6a5fd3dc2f

Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition

Authors: Bernhard Kuhle, Marscha Hirschi, Lili K. Doerfel, Gabriel C. Lander, Paul Schimmel

Source: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1927bea390454aeb94586ab2d058d497

Importance of the Cysteine-Rich Domain of Snake Venom Prothrombin Activators: Insights Gained from Synthetic Neutralizing Antibodies

Authors: Laetitia E. Misson Mindrebo, Jeffrey T. Mindrebo, Quoc Tran, Mark C. Wilkinson, Jessica M. Smith, Megan Verma, Nicholas R. Casewell, Gabriel C. Lander, Joseph G. Jardine

Source: Toxins, Vol 16, Iss 8, p 361 (2024)

Subject Terms: snake venom metalloproteinases, prothrombin activator, Echis, recombinant antivenom, neutralizing antibody, cysteine-rich domain, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2072-6651/16/8/361; https://doaj.org/toc/2072-6651

Access URL: https://doaj.org/article/50e022fa1a7441a6b54a54493eb0306b

Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA

Authors: Bernhard Kuhle, Marscha Hirschi, Lili K. Doerfel, Gabriel C. Lander, Paul Schimmel

Source: Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c61de2c5906644379fa90b8007176bd0

The YΦ motif defines the structure-activity relationships of human 20S proteasome activators

Authors: Kwadwo A. Opoku-Nsiah, Andres H. de la Pena, Sarah K. Williams, Nikita Chopra, Andrej Sali, Gabriel C. Lander, Jason E. Gestwicki

Source: Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/12967c8972e54d50b98fad4d225e07ce

Structures of the human LONP1 protease reveal regulatory steps involved in protease activation

Authors: Mia Shin, Edmond R. Watson, Albert S. Song, Jeffrey T. Mindrebo, Scott J. Novick, Patrick R. Griffin, R. Luke Wiseman, Gabriel C. Lander

Source: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/bb66b8ea8165482a8ae94b393309ce0d

AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex

Authors: Marscha Hirschi, Wang-Ting Lu, Andrew Santiago-Frangos, Royce Wilkinson, Sarah M. Golden, Alan R. Davidson, Gabriel C. Lander, Blake Wiedenheft

Source: Nature Communications, Vol 11, Iss 1, Pp 1-6 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d3c21875e57643ea9c2043b059ad21af

Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel

Authors: Ying Yin, Mengyu Wu, Allen L. Hsu, William F. Borschel, Mario J. Borgnia, Gabriel C. Lander, Seok-Yong Lee

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/6260631b549d4c0287f9fa8aff10adbc

High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM

Authors: Mark A. Herzik, Mengyu Wu, Gabriel C. Lander

Source: Nature Communications, Vol 10, Iss 1, Pp 1-9 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/082a304c2b0a4f3b94de0ccbd7867848

Conformational ensemble of the human TRPV3 ion channel

Authors: Lejla Zubcevic, Mark A. Herzik, Mengyu Wu, William F. Borschel, Marscha Hirschi, Albert S. Song, Gabriel C. Lander, Seok-Yong Lee

Source: Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/2ea7563e099f422d909405e9c45dad14

The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading

Authors: Brooke M. Gardner, Dominic T. Castanzo, Saikat Chowdhury, Goran Stjepanovic, Matthew S. Stefely, James H. Hurley, Gabriel C. Lander, Andreas Martin

Source: Nature Communications, Vol 9, Iss 1, Pp 1-15 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/4061a2c4972642c8b618677d741846cd

A guided approach for subtomogram averaging of challenging macromolecular assemblies

Authors: Benjamin Basanta, Saikat Chowdhury, Gabriel C. Lander, Danielle A. Grotjahn

Source: Journal of Structural Biology: X, Vol 4, Iss , Pp 100041- (2020)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590152420300271; https://doaj.org/toc/2590-1524

Access URL: https://doaj.org/article/2ac18ae3c1474411bf691d02ff9f034f

Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV

Authors: Mengyu Wu, Gabriel C. Lander, Mark A. Herzik, Jr.

Source: Journal of Structural Biology: X, Vol 4, Iss , Pp 100020- (2020)

Subject Terms: Cryo-EM, Single particle cryo-EM, 200 keV, Electron microscopy, Microscope aberrations, Two-condenser lens, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590152420300027; https://doaj.org/toc/2590-1524

Access URL: https://doaj.org/article/3770620418bf4cebab35038e831371fe

The Rod-Shaped ATG2A-WIPI4 Complex Tethers Membranes In Vitro

Authors: Takanori Otomo, Saikat Chowdhury, Gabriel C. Lander

Source: Contact, Vol 1 (2018)

Subject Terms: Biology (General), QH301-705.5, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/2515-2564

Access URL: https://doaj.org/article/73117848c7c2447396b69efb47211f1b

Fabrication of Monolayer Graphene-Coated Grids for Cryoelectron Microscopy

Authors: Benjamin Basanta, author¹, Wenqian Chen, author¹, Daniel E. Pride, author¹, Gabriel C. Lander, author¹

Source: Journal of Visualized Experiments. (199)

Availability: http://www.jove.com/video/65702

Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing

Authors: Jennifer L Fribourgh, Ashutosh Srivastava, Colby R Sandate, Alicia K Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, Megan R Torgrimson, Gian Carlo G Parico, Sarvind Tripathi, Ning Zheng, Gabriel C Lander, Tsuyoshi Hirota, Florence Tama, Carrie L Partch

Source: eLife, Vol 9 (2020)

Subject Terms: circadian rhythms, x-ray crystallography, cryo-electron microscopy, molecular dynamics, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/55275; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/fea51974e20a400a90ed8488c058c791

Specific lid-base contacts in the 26s proteasome control the conformational switching required for substrate degradation

Authors: Eric R Greene, Ellen A Goodall, Andres H de la Peña, Mary E Matyskiela, Gabriel C Lander, Andreas Martin

Source: eLife, Vol 8 (2019)

Subject Terms: 26S proteasome, ubiquitin-proteasome System, AAA+ ATPase, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/49806; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/dbd8bfb1de2c493ea1b997a537b4f81a

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition

Authors: Corey M Dambacher, Evan J Worden, Mark A Herzik Jr., Andreas Martin, Gabriel C Lander

Source: eLife, Vol 5 (2016)

Subject Terms: proteasome, deubiquitination, cryoEM, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/13027; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/2c180e2fda1940f5a4029f205300f727

Molecular architecture of human polycomb repressive complex 2

Authors: Claudio Ciferri, Gabriel C Lander, Alessio Maiolica, Franz Herzog, Ruedi Aebersold, Eva Nogales

Source: eLife, Vol 1 (2012)

Subject Terms: cryo-EM, Gene silencing, labeling, chemical cross-linking, chromatin, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/00005; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/243e5f39fded4921861ac9d3467da036