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OPUS-Rota5: A highly accurate protein side-chain modeling method with 3D-Unet and RotaFormer Structure (IF 5.7) Pub Date : 2024-04-23 Gang Xu, Zhenwei Luo, Yaming Yan, Qinghua Wang, Jianpeng Ma
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Mapping structural and dynamic divergence across the MBOAT family Structure (IF 5.7) Pub Date : 2024-04-17 T. Bertie Ansell, Megan Healy, Claire E. Coupland, Mark S.P. Sansom, Christian Siebold
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Molecular basis for pH sensing in the KDEL trafficking receptor Structure (IF 5.7) Pub Date : 2024-04-15 Zhiyi Wu, Kathryn Smith, Andreas Gerondopoulos, Tomoaki Sobajima, Joanne L. Parker, Francis A. Barr, Simon Newstead, Philip C. Biggin
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Structural basis for the immune recognition and selectivity of the immune receptor PVRIG for ligand Nectin-2 Structure (IF 5.7) Pub Date : 2024-04-15 Songtao Hu, Pu Han, Meiyu Wang, Xiaoqing Cao, Hao Liu, Shuailong Zhang, Shuijun Zhang, Jun Liu, Yi Han, Jinhe Xiao, Qiang Chen, Kai Miao, Jianxun Qi, Shuguang Tan, George Fu Gao, Han Wang
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Cryo-EM structure of flagellotropic bacteriophage Chi Structure (IF 5.7) Pub Date : 2024-04-12 Ravi R. Sonani, Nathaniel C. Esteves, Birgit E. Scharf, Edward H. Egelman
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Human V-ATPase function is positively and negatively regulated by TLDc proteins Structure (IF 5.7) Pub Date : 2024-04-08 Rebecca A. Oot, Stephan Wilkens
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The cryo-EM structure of trypanosome 3-methylcrotonyl-CoA carboxylase provides mechanistic and dynamic insights into its enzymatic function Structure (IF 5.7) Pub Date : 2024-04-08 Adrián Plaza-Pegueroles, Inna Aphasizheva, Ruslan Aphasizhev, Carlos Fernández-Tornero, Federico M. Ruiz
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Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism Structure (IF 5.7) Pub Date : 2024-04-05 Mattia D'Agostino, Angelita Simonetti, Stefano Motta, Philippe Wolff, Alice Romagnoli, Astra Piccinini, Francesco Spinozzi, Daniele Di Marino, Anna La Teana, Eric Ennifar
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Cryo-EM structures reveal two allosteric inhibition modes of PI3KαH1047R involving a re-shaping of the activation loop Structure (IF 5.7) Pub Date : 2024-04-05 Xiuliang Huang, Kailiang Wang, Jing Han, Xiumei Chen, Zhenglin Wang, Tianlun Wu, Bo Yu, Feng Zhao, Xinjuan Wang, Huijuan Li, Zhi Xie, Xiaotian Zhu, Wenge Zhong, Xiaoming Ren
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A glimpse into Giardia lamblia unique translational machinery Structure (IF 5.7) Pub Date : 2024-04-04 Jailson Brito Querido
Eiler et al. used cryo-electron microscopy to determine a 2.49 Å resolution structure of Giardia lamblia 80S ribosome bound to tRNA, mRNA, and the anti-protozoal drug emetine. The structure reveals some critical aspects of translation in G. lamblia, including the lack of ribosomal protein RACK1, and how emetine blocks translation by interacting with both the ribosome and mRNA.
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Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus Structure (IF 5.7) Pub Date : 2024-04-04 Yaping Shen, Yaning Li, Renhong Yan
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MLL4 binds TET3 Structure (IF 5.7) Pub Date : 2024-04-04 Dustin C. Becht, Sk Abdul Mohid, Ji-Eun Lee, Mohamad Zandian, Caroline Benz, Soumi Biswas, Vikrant Kumar Sinha, Ylva Ivarsson, Kai Ge, Yi Zhang, Tatiana G. Kutateladze
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Full-length αIIbβ3 cryo-EM structure reveals intact integrin initiate-activation intrinsic architecture Structure (IF 5.7) Pub Date : 2024-04-04 Tong Huo, Hongjiang Wu, Zeinab Moussa, Mehmet Sen, Valerie Dalton, Zhao Wang
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Disorder in CENP-ACse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore Structure (IF 5.7) Pub Date : 2024-04-01 Shivangi Shukla, Anusri Bhattacharya, Parveen Sehrawat, Prakhar Agarwal, Rahul Shobhawat, Nikita Malik, Kalaiyarasi Duraisamy, Nithyakalyani Sri Rangan, Ramakrishna V. Hosur, Ashutosh Kumar
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High-resolution cryo-EM of a small protein complex: The structure of the human CDK-activating kinase Structure (IF 5.7) Pub Date : 2024-04-01 Basil J. Greber
The human CDK-activating kinase (CAK) is a multifunctional protein complex and key regulator of cell growth and division. Because of its critical functions in regulating the cell cycle and transcription initiation, it is a key target for multiple cancer drug discovery programs. However, the structure of the active human CAK, insights into its regulation, and its interactions with cellular substrates
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Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4 Structure (IF 5.7) Pub Date : 2024-03-26 Meng Yuan, Linghang Peng, Deli Huang, Amanda Gavin, Fangkun Luan, Jenny Tran, Ziqi Feng, Xueyong Zhu, Jeanne Matteson, Ian A. Wilson, David Nemazee
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The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA Structure (IF 5.7) Pub Date : 2024-03-25 Jay Z. Yin, Alexander F.A. Keszei, Scott Houliston, Frantisek Filandr, Jonah Beenstock, Salima Daou, Julia Kitaygorodsky, David C. Schriemer, Mohammad T. Mazhab-Jafari, Anne-Claude Gingras, Frank Sicheri
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Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension Structure (IF 5.7) Pub Date : 2024-03-22 Benjamin J. Lane, Yue Ma, Nana Yan, Bolin Wang, Katrin Ackermann, Theodoros K. Karamanos, Bela E. Bode, Christos Pliotas
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Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin Structure (IF 5.7) Pub Date : 2024-03-21 Ewa Niedzialkowska, Lucas A. Runyan, Elena Kudryashova, Edward H. Egelman, Dmitri S. Kudryashov
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Structural insights into a functional unit from an immunogenic mollusk hemocyanin Structure (IF 5.7) Pub Date : 2024-03-20 Sebastián M. Muñoz, Gabriel Vallejos-Baccelliere, Augusto Manubens, Michelle L. Salazar, Andrey F.Z. Nascimento, Patricio Tapia-Reyes, Claudio Meneses, Andre L.B. Ambrosio, María Inés Becker, Victoria Guixé, Victor Castro-Fernandez
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A suite of designed protein cages using machine learning and protein fragment-based protocols Structure (IF 5.7) Pub Date : 2024-03-20 Kyle Meador, Roger Castells-Graells, Roman Aguirre, Michael R. Sawaya, Mark A. Arbing, Trent Sherman, Chethaka Senarathne, Todd O. Yeates
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PMSPcnn: Predicting protein stability changes upon single point mutations with convolutional neural network Structure (IF 5.7) Pub Date : 2024-03-19 Xiaohan Sun, Shuang Yang, Zhixiang Wu, Jingjie Su, Fangrui Hu, Fubin Chang, Chunhua Li
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DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity Structure (IF 5.7) Pub Date : 2024-03-19 Bryan D. Ryder, Elizaveta Ustyantseva, David R. Boyer, Ayde Mendoza-Oliva, Mikołaj I. Kuska, Paweł M. Wydorski, Paulina Macierzyńska, Nabil Morgan, Michael R. Sawaya, Marc I. Diamond, Harm H. Kampinga, Lukasz A. Joachimiak
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Structural insights into the catalytic mechanism of the AP endonuclease AtARP Structure (IF 5.7) Pub Date : 2024-03-18 Wenting Guo, Weijun Wu, Yan Wen, Yuan Gao, Shuting Zhuang, Chunyan Meng, Haitao Chen, Zhipeng Zhao, Kaishun Hu, Baixing Wu
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Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I Structure (IF 5.7) Pub Date : 2024-03-18 Daniel Wohlwend, Luca Mérono, Sarah Bucka, Kevin Ritter, Henning J. Jessen, Thorsten Friedrich
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Structural insights into thermophilic chaperonin complexes Structure (IF 5.7) Pub Date : 2024-03-15 Zengwei Liao, Chai C. Gopalasingam, Masafumi Kameya, Christoph Gerle, Hideki Shigematsu, Masaharu Ishii, Takatoshi Arakawa, Shinya Fushinobu
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Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank Structure (IF 5.7) Pub Date : 2024-03-14 Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A. Ramelot, Monica Sekharan, James Tolchard, John D. Westbrook, Benjamin Bardiaux, Charles D. Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K. Burley, Genji Kurisu, Jeffrey C. Hoch, Gaetano T. Montelione, Jasmine Y. Young
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Correlative cryo-soft X-ray tomography and cryo-structured illumination microscopy reveal changes to lysosomes in amyloid-β-treated neurons Structure (IF 5.7) Pub Date : 2024-03-11 Karen E. Marshall, Kurtis Mengham, Matthew C. Spink, Lyra Vania, Hannah Jane Pollard, Michele C. Darrow, Elizabeth Duke, Maria Harkiolaki, Louise C. Serpell
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CHCHD4 binding affects the active site of apoptosis inducing factor (AIF): Structural determinants for allosteric regulation Structure (IF 5.7) Pub Date : 2024-03-08 Elisa Fagnani, Paolo Cocomazzi, Sara Pellegrino, Gabriella Tedeschi, Francesca Grassi Scalvini, Federica Cossu, Stefano Da Vela, Alessandro Aliverti, Eloise Mastrangelo, Mario Milani
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Structural insights into the unique pH-responsive characteristics of the anti-TIGIT therapeutic antibody Ociperlimab Structure (IF 5.7) Pub Date : 2024-03-08 Jian Sun, Xiangxiang Zhang, Liu Xue, Liang Cheng, Jing Zhang, Xin Chen, Zhirong Shen, Kang Li, Lai Wang, Chichi Huang, Jing Song
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Locally misfolded HER2 expressed on cancer cells is a promising target for development of cancer-specific antibodies Structure (IF 5.7) Pub Date : 2024-03-08 Takao Arimori, Emiko Mihara, Hiroyuki Suzuki, Tomokazu Ohishi, Tomohiro Tanaka, Mika K. Kaneko, Junichi Takagi, Yukinari Kato
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Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes Structure (IF 5.7) Pub Date : 2024-03-07 Rishi Kumar Mishra, Prafful Sharma, Faisal Tarique Khaja, Adwaith B. Uday, Tanweer Hussain
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Heterogeneous sampled subgraph neural networks with knowledge distillation to enhance double-blind compound-protein interaction prediction Structure (IF 5.7) Pub Date : 2024-03-05 Ying Xia, Xiaoyong Pan, Hong-Bin Shen
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The mechanism and energetics of the dynein priming stroke Structure (IF 5.7) Pub Date : 2024-03-01 Mert Golcuk, Sema Zeynep Yilmaz, Ahmet Yildiz, Mert Gur
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AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes Structure (IF 5.7) Pub Date : 2024-02-29 Robert T. McDonnell, Adrian H. Elcock
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Cryo-EM structure and molecular dynamic simulations explain the enhanced stability and ATP activity of the pathological chaperonin mutant Structure (IF 5.7) Pub Date : 2024-02-26 Aiza Syed, Jihang Zhai, Baolin Guo, Yuan Zhao, Joseph Che-Yen Wang, Lingling Chen
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X-rays, electrons, and neutrons as probes of atomic matter Structure (IF 5.7) Pub Date : 2024-02-26 Matthias Bochtler
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Membrane mimetic-dependence of GPCR energy landscapes Structure (IF 5.7) Pub Date : 2024-02-23 Naveen Thakur, Arka Prabha Ray, Beining Jin, Nessa Pesaran Afsharian, Edward Lyman, Zhan-Guo Gao, Kenneth A. Jacobson, Matthew T. Eddy
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Insertases scramble lipids: Molecular simulations of MTCH2 Structure (IF 5.7) Pub Date : 2024-02-19 Ladislav Bartoš, Anant K. Menon, Robert Vácha
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EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry Structure (IF 5.7) Pub Date : 2024-02-16 Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
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Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains Structure (IF 5.7) Pub Date : 2024-02-09 Ye-Jun Peng, Yuxing Chen, Cong-Zhao Zhou, Wei Miao, Yong-Liang Jiang, Xiaoli Zeng, Cheng-Cai Zhang
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Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: Structural basis of their function Structure (IF 5.7) Pub Date : 2024-02-06 Martin Klima, Milan Dejmek, Vojtech Duchoslav, Andrea Eisenreichova, Michal Sala, Karel Chalupsky, Dominika Chalupska, Barbora Novotná, Gabriel Birkuš, Radim Nencka, Evzen Boura
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Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding Structure (IF 5.7) Pub Date : 2024-02-06 Paweł P. Knejski, Satchal K. Erramilli, Anthony A. Kossiakoff
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De novo design of cavity-containing proteins with a backbone-centered neural network energy function Structure (IF 5.7) Pub Date : 2024-02-06 Yang Xu, Xiuhong Hu, Chenchen Wang, Yongrui Liu, Quan Chen, Haiyan Liu
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Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma Structure (IF 5.7) Pub Date : 2024-02-02 Longying Jiang, Xueke Liu, Xujun Liang, Shuyan Dai, Hudie Wei, Ming Guo, Zhuchu Chen, Desheng Xiao, Yongheng Chen
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Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2 Structure (IF 5.7) Pub Date : 2024-02-02 William J. Bradshaw, Emma C. Kennedy, Tiago Moreira, Luke A. Smith, Rod Chalk, Vittorio L. Katis, Justin L.P. Benesch, Paul E. Brennan, Emma J. Murphy, Opher Gileadi
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Understanding cytokinesis interaction by interaction Structure (IF 5.7) Pub Date : 2024-02-01 Andreas Haahr Larsen
In this issue of Structure, Hall et al.1 investigate the binding modes of anillin-like Mid1. During cytokinesis, Mid1 connects the contractile ring to the plasma membrane. Using computer simulations, the authors demonstrated how this connection is established via the L3 loop of the C2 domain.
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CELSR1, a core planar cell polarity protein, features a weakly adhesive and flexible cadherin ectodomain Structure (IF 5.7) Pub Date : 2024-02-01 Elakkiya Tamilselvan, Marcos Sotomayor
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Cryo-EM research in India Structure (IF 5.7) Pub Date : 2024-02-01 Arun K. Shukla, Manidipa Banerjee, Appu K. Singh, Aravind Penmatsa, Somnath Dutta, Ruchi Anand, Minhajuddin Sirajuddin, Shanti Swaroop Srivastava
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The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function Structure (IF 5.7) Pub Date : 2024-01-18 Daniel R. Eiler, Brian T. Wimberly, Danielle Y. Bilodeau, J. Matthew Taliaferro, Philip Reigan, Olivia S. Rissland, Jeffrey S. Kieft
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The series of conformational states adopted by rotorless F1-ATPase during its hydrolysis cycle Structure (IF 5.7) Pub Date : 2024-01-17 Meghna Sobti, Hiroshi Ueno, Simon H.J. Brown, Hiroyuki Noji, Alastair G. Stewart
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Structural determinants for tRNA selective cleavage by RNase 2/EDN Structure (IF 5.7) Pub Date : 2024-01-15 Jiarui Li, Xincheng Kang, Irene Guidi, Lu Lu, Pablo Fernández-Millán, Guillem Prats-Ejarque, Ester Boix
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Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1 Structure (IF 5.7) Pub Date : 2024-01-15 Tatsuhiko Ozawa, Yoshiki Ikeda, Liuan Chen, Rigel Suzuki, Atsushi Hoshino, Akira Noguchi, Shunsuke Kita, Yuki Anraku, Emiko Igarashi, Yumiko Saga, Noriko Inasaki, Shunta Taminishi, Jiei Sasaki, Yuhei Kirita, Hideo Fukuhara, Katsumi Maenaka, Takao Hashiguchi, Takasuke Fukuhara, Kenichi Hirabayashi, Hideki Tani, Hiroyuki Kishi, Hideki Niimi
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Structural insight into CD93 recognition by IGFBP7 Structure (IF 5.7) Pub Date : 2024-01-12 Yueming Xu, Yi Sun, Yuwen Zhu, Gaojie Song
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Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders Structure (IF 5.7) Pub Date : 2024-01-09 Dora Buzas, Huan Sun, Christine Toelzer, Sathish K.N. Yadav, Ufuk Borucu, Gunjan Gautam, Kapil Gupta, Joshua C. Bufton, Julien Capin, Richard B. Sessions, Frederic Garzoni, Imre Berger, Christiane Schaffitzel
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CRD: A de novo design algorithm for the prediction of cognate protein receptors for small molecule ligands Structure (IF 5.7) Pub Date : 2024-01-08 Santhosh Sankar, Sneha Vasudevan, Nagasuma Chandra
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Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy Structure (IF 5.7) Pub Date : 2024-01-08 Kayo Imamura, Ken-Ichi Akagi, Yohei Miyanoiri, Hirokazu Tsujimoto, Takatsugu Hirokawa, Hideo Ashida, Kaori Murakami, Asuka Inoue, Ryoji Suno, Takahisa Ikegami, Naotaka Sekiyama, So Iwata, Takuya Kobayashi, Hidehito Tochio
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Multiple masks of a Shigella podophage Structure (IF 5.7) Pub Date : 2024-01-04 Yong-Liang Jiang, Cong-Zhao Zhou
In this issue of Structure, Subramanian et al. present the cryo-EM structure of Shigella podophage HRP29, which possesses a T7-like tail complex surrounded by six P22/Sf6-like tailspikes and two unique decoration proteins. These colorful masks of HRP29 record the frequent events of horizontal gene transfer during evolution.
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Interplay between intrinsic flexibility and sugar coating in Contactin-2 homodimerization Structure (IF 5.7) Pub Date : 2024-01-04 Mehmet Sen
In this issue of Structure, Chataigner et al. reveal that Contactin-2’s homotypic interaction, a glycosylation-dependent process, generates a broad conformational landscape. This structural plasticity, driven by conformational equilibria and sugar coating, facilitates adaptation to diverse ligands and environmental conditions, highlighting its dynamic role in neuronal function.
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From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all Structure (IF 5.7) Pub Date : 2024-01-04 Yui Tik Pang, Lixinhao Yang, James C. Gumbart
In this issue of Structure, Heo and Feig present cg2all, a novel deep-learning model capable of efficiently predicting all-atom protein structures from coarse-grained (CG) representations. The model maintains high accuracy, even when the CG model is simplified to a single bead per residue, and has a number of promising applications.