Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

Mechanism of metal ion activation of the diphtheria toxin repressor DtxR

D'Aquino, J. A., Tetenbaum-Novatt, J., White, A., Berkovitch, F., & Ringe, D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500908102 · Cited by 57

Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD

Eichhorn, E., Davey, C. A., Sargent, D. F., Leisinger, T., & Richmond, T. J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01069-0 · Cited by 57

Rac regulates its effector phospholipase Cγ2 through interaction with a split pleckstrin homology domain

Walliser, C., Retlich, M., Harris, R., Everett, K. L., Josephs, M. B., Vatter, P., Esposito, D., Driscoll, P. C., Katan, M., Gierschik, P., et al. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803316200 · Cited by 56

Insights into the Phosphoregulation of β‐Secretase Sorting Signal by the VHS Domain of GGA1

Shiba, T., Kametaka, S., Kawasaki, M., Shibata, M., Waguri, S., Uchiyama, Y., & Wakatsuki, S. (2004) · Traffic · doi:10.1111/j.1600-0854.2004.00188.x · Cited by 56

Structural insights into the effects of 2’-5’ linkages on the RNA duplex

Sheng, J., Li, L., Engelhart, A. E., Gan, J., Wang, J., & Szostak, J. W. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317799111 · Cited by 50

Further insight into substrate recognition by USP7: structural and biochemical analysis of the HdmX and Hdm2 interactions with USP7.

Sarkari, F., La Delfa, A., Arrowsmith, C. H., Frappier, L., Sheng, Y., & Saridakis, V. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.017 · Cited by 54

Crystal Structure of an Archaeal Actin Homolog

Roeben, A., Kofler, C., Nagy, I., Nickell, S., Ulrich Hartl, F., & Bracher, A. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.096 · Cited by 53

Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1

Dove, K. K., Olszewski, J. L., Martino, L., Duda, D. M., Wu, X. S., Miller, D. J., Reiter, K. H., Rittinger, K., Schulman, B. A., & Klevit, R. E. (2017) · Structure · doi:10.1016/j.str.2017.04.013 · Cited by 52

Structural Insight into Modest Binding of a Non-PXXP Ligand to the Signal Transducing Adaptor Molecule-2 Src Homology 3 Domain

Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., & Tanaka, N. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m306677200 · Cited by 51

Crystal Structure of the Tp34 (TP0971) Lipoprotein of Treponema pallidum

Deka, R. K., Brautigam, C. A., Tomson, F. L., Lumpkins, S. B., Tomchick, D. R., Machius, M., & Norgard, M. V. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m610215200 · Cited by 50

Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: a 1.9 Å Crystal Structure of the Active Form of ScpA.

Kagawa, T. F., O'Connell, M. R., Mouat, P., Paoli, M., O'Toole, P. W., & Cooney, J. C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.074 · Cited by 50

Regulation of apoptosis by an intrinsically disordered region of Bcl-xL

Follis, A. V., Llambi, F., Kalkavan, H., Yao, Y., Phillips, A. H., Park, C.-G., Marassi, F. M., Green, D. R., & Kriwacki, R. W. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0011-x · Cited by 47

X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

Jitsumori, K., Omi, R., Kurihara, T., Kurata, A., Mihara, H., Miyahara, I., Hirotsu, K., & Esaki, N. (2009) · Journal of Bacteriology · doi:10.1128/jb.01654-08 · Cited by 50

Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex

Lansdon, E. B., Samuel, D., Lagpacan, L., Brendza, K. M., White, K. L., Hung, M., Liu, X., Boojamra, C. G., Mackman, R. L., Cihlar, T., et al. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.02.019 · Cited by 49

Phosphorylation of conserved phosphoinositide binding pocket regulates sorting nexin membrane targeting

Lenoir, M., Ustunel, C., Rajesh, S., Kaur, J., Moreau, D., Gruenberg, J., & Overduin, M. (2018) · Nature Communications · doi:10.1038/s41467-018-03370-1 · Cited by 49

A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex

Banerjee, A., & Verdine, G. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603644103 · Cited by 48

Structural Evidence for a Sequential Release Mechanism for Activation of Heterotrimeric G Proteins

Kapoor, N., Menon, S. T., Chauhan, R., Sachdev, P., & Sakmar, T. P. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.08.043 · Cited by 47

Solution Structure and Dynamics of the Small GTPase RalB in Its Active Conformation: Significance for Effector Protein Binding

Fenwick, R. B., Prasannan, S., Campbell, L. J., Nietlispach, D., Evetts, K. A., Camonis, J., Mott, H. R., & Owen, D. (2009) · Biochemistry · doi:10.1021/bi802129d · Cited by 47

Native interface of the SAM domain polymer of TEL

Tran, H. H., Kim, C. A., Faham, S., Siddall, M.-C., & Bowie, J. U. (2002) · BMC Structural Biology · doi:10.1186/1472-6807-2-5 · Cited by 42

Dimeric Rous Sarcoma Virus Capsid Protein Structure Relevant to Immature Gag Assembly

Nandhagopal, N., Simpson, A. A., Johnson, M. C., Francisco, A. B., Schatz, G. W., Rossmann, M. G., & Vogt, V. M. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.10.034 · Cited by 44

Functional and structural characterization of a dense core secretory granule sorting domain from the PC1/3 protease

Dikeakos, J. D., Di Lello, P., Lacombe, M.-J., Ghirlando, R., Legault, P., Reudelhuber, T. L., & Omichinski, J. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809576106 · Cited by 40

Structural Analysis of Cytochrome P450 105N1 Involved in the Biosynthesis of the Zincophore, Coelibactin

Zhao, B., Moody, S. C., Hider, R. C., Lei, L., Kelly, S. L., Waterman, M. R., & Lamb, D. C. (2012) · International Journal of Molecular Sciences · doi:10.3390/ijms13078500 · Cited by 42

Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features.

Lang, R., Braun, M., Sounni, N. E., Noel, A., Frankenne, F., Foidart, J.-M., Bode, W., & Maskos, K. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.022 · Cited by 42

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Henry, N., Krammer, E.-M., Stengel, F., Adams, Q., Van Liefferinge, F., Hubin, E., Chaves, R., Efremov, R., Aebersold, R., Vandenbussche, G., et al. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006165 · Cited by 42

Discovery of Umibecestat (CNP520): A Potent, Selective, and Efficacious β-Secretase (BACE1) Inhibitor for the Prevention of Alzheimer’s Disease

Machauer, R., Lueoend, R., Hurth, K., Veenstra, S. J., Rueeger, H., Voegtle, M., Tintelnot-Blomley, M., Rondeau, J.-M., Jacobson, L. H., Laue, G., et al. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01300 · Cited by 40

Molecular replacement: tricks and treats

Abergel, C. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913015291 · Cited by 36

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

Aiyer, S., Swapna, G. V. T., Ma, L.-C., Liu, G., Hao, J., Chalmers, G., Jacobs, B. C., Montelione, G. T., & Roth, M. J. (2021) · Structure · doi:10.1016/j.str.2021.01.010 · Cited by 35

Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5

Lemak, A., Yee, A., Wu, H., Yap, D., Zeng, H., Dombrovski, L., Houliston, S., Aparicio, S., & Arrowsmith, C. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077020 · Cited by 36

Impact of Retinal Disease-Associated RPE65 Mutations on Retinoid Isomerization

Bereta, G., Kiser, P. D., Golczak, M., Sun, W., Heon, E., Saperstein, D. A., & Palczewski, K. (2008) · Biochemistry · doi:10.1021/bi800905v · Cited by 36

Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2

Cantara, W. A., Bilbille, Y., Kim, J., Kaiser, R., Leszczyńska, G., Malkiewicz, A., & Agris, P. F. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.12.054 · Cited by 36

Binding of More Than One Retinoid to Visual Opsins

Makino, C. L., Riley, C. K., Looney, J., Crouch, R. K., & Okada, T. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.08.003 · Cited by 33

Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

Shen, A., Higgins, D. E., & Panne, D. (2009) · Structure · doi:10.1016/j.str.2009.02.018 · Cited by 35

Structure of NFAT Bound to DNA as a Monomer

Stroud, J. C., & Chen, L. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.09.065 · Cited by 35

Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5

Tao, X., & Tong, L. (2007) · Protein Science · doi:10.1110/ps.062712807 · Cited by 31

Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications

Goydel, R. S., Weber, J., Peng, H., Qi, J., Soden, J., Freeth, J., Park, H., & Rader, C. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.012791 · Cited by 34

Instability of the Human Cytochrome P450 Reductase A287P Variant Is the Major Contributor to Its Antley-Bixler Syndrome-like Phenotype

McCammon, K. M., Panda, S. P., Xia, C., Kim, J.-J. P., Moutinho, D., Kranendonk, M., Auchus, R. J., Lafer, E. M., Ghosh, D., Martasek, P., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.716019 · Cited by 33

Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms

Dennis, R. J., Micossi, E., McCarthy, J., Moe, E., Gordon, E. J., Kozielski-Stuhrmann, S., Leonard, G. A., & McSweeney, S. (2006) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309106008402 · Cited by 30

Structural and sequencing analysis of local target DNA recognition by MLV integrase

Aiyer, S., Rossi, P., Malani, N., Schneider, W. M., Chandar, A., Bushman, F. D., Montelione, G. T., & Roth, M. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv410 · Cited by 25

Mechanism of N10‐formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors

Celeste, L. R., Chai, G., Bielak, M., Minor, W., Lovelace, L. L., & Lebioda, L. (2012) · Protein Science · doi:10.1002/pro.2005 · Cited by 27

Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation

Park, S.-Y., Jin, W., Woo, J. R., & Shoelson, S. E. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.217323 · Cited by 25

Evolution of Enzymatic Activities in the Enolase Superfamily: Identification of the General Acid Catalyst in theActive Site of d-Glucarate Dehydratase from Escherichia coli,

Gulick, A. M., Hubbard, B. K., Gerlt, J. A., & Rayment, I. (2001) · Biochemistry · doi:10.1021/bi010733b · Cited by 25

OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors

Xu, G., Wang, Q., & Ma, J. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbab529 · Cited by 24

Structural Studies of a Complex Between Endothelial Nitric Oxide Synthase and Calmodulin at Physiological Calcium Concentration

Piazza, M., Dieckmann, T., & Guillemette, J. G. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00821 · Cited by 23

Two Distinct Binding Modes Define the Interaction of Brox with the C-Terminal Tails of CHMP5 and CHMP4B

Mu, R., Dussupt, V., Jiang, J., Sette, P., Rudd, V., Chuenchor, W., Bello, N. F., Bouamr, F., & Xiao, T. S. (2012) · Structure · doi:10.1016/j.str.2012.03.001 · Cited by 23

Large-scale discovery, analysis and design of protein energy landscapes

Ferrari, Á. J. R., Dixit, S. M., Thibeault, J., Garcia, M., Houliston, S., Ludwig, R. W., Notin, P., Phoumyvong, C. M., Martell, C. M., Jung, M. D., et al. (2026) · Nature · doi:10.1038/s41586-026-10465-z · Cited by 22

X‐ray structure of an M. jannaschii DNA‐binding protein: Implications for antibiotic resistance in S. aureus

Ray, S. S., Bonanno, J. B., Chen, H., de Lencastre, H., Wu, S., Tomasz, A., & Burley, S. K. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10272 · Cited by 21

Assembly and disassembly of Aspergillus fumigatus conidial rodlets

Valsecchi, I., Lai, J. I., Stephen-Victor, E., Pillé, A., Beaussart, A., Lo, V., Pham, C. L. L., Aimanianda, V., Kwan, A. H., Duchateau, M., et al. (2019) · The Cell Surface · doi:10.1016/j.tcsw.2019.100023 · Cited by 46

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

Wang, L., Zhang, J., Wang, D., & Song, C. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009972 · Cited by 18

Apo and Calcium-bound Crystal Structures of Alpha-11 Giardin, an Unusual Annexin from Giardia lamblia

Pathuri, P., Nguyen, E. T., Svärd, S. G., & Luecke, H. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.02.016 · Cited by 18

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26269 · Cited by 15

HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-Terminal Tail in HIV-1 Integration

Li, M., Li, Z., Chen, X., Cui, Y., Engelman, A. N., & Craigie, R. (2024) · Viruses · doi:10.3390/v16071166 · Cited by 12

Central Cavity of Fructose-1,6-bisphosphatase and the Evolution of AMP/Fructose 2,6-bisphosphate Synergism in Eukaryotic Organisms

Gao, Y., Shen, L., & Honzatko, R. B. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.548586 · Cited by 11

The Structure of the RLIP76 RhoGAP-Ral Binding Domain Dyad: Fixed Position of the Domains Leads to Dual Engagement of Small G Proteins at the Membrane

Rajasekar, K. V., Campbell, L. J., Nietlispach, D., Owen, D., & Mott, H. R. (2013) · Structure · doi:10.1016/j.str.2013.09.007 · Cited by 11

Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR

Kuschert, S., Stroet, M., Chin, Y. K.-Y., Conibear, A. C., Jia, X., Lee, T., Bartling, C. R. O., Strømgaard, K., Güntert, P., Rosengren, K. J., et al. (2023) · Magnetic Resonance · doi:10.5194/mr-4-57-2023 · Cited by 9

Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide 15 N( 1 H) NMR Relaxation

Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Orekhov, V., & Agback, P. (2025) · doi:10.1101/2025.02.07.637034 · Cited by 6

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction

Boyd, L. F., Jiang, J., Ahmad, J., Natarajan, K., & Margulies, D. H. (2024) · The Journal of Immunology · doi:10.4049/jimmunol.2300839 · Cited by 6

Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

(2024) · doi:10.1038/s42003-024-07330-y · Cited by 6

Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation

Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Agback, P., & Orekhov, V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26188917 · Cited by 6

Influence of Stereochemistry in a Local Approach for Calculating Protein Conformations

da Rocha, W., Liberti, L., Mucherino, A., & Malliavin, T. E. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01232 · Cited by 3

Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1

(2023) · doi:10.1016/j.str.2023.05.012 · Cited by 3

Identifying androsterone (ADT) as a cognate substrate for human dehydroepiandrosterone sulfotransferase (DHEA-ST) important for steroid homeostasis

Chang, H.-J., Shi, R., Rehse, P., & Lin, S.-X. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310446200 · Cited by 1

Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1

Fowler, N. J., Albalwi, M. F., Lee, S., Hounslow, A. M., & Williamson, M. P. (2022) · doi:10.1101/2022.08.29.505644